From b500fa9ce69b575b83e7b1514aeb23b5895ba610 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 15 Sep 2010 11:35:15 +0000
Subject: [PATCH] LMS-1746 Checking in again (last time didn't take).
SVN: 17841
---
.../api/v1/GeneralInformationService.java | 20 +++
.../v1/GeneralInformationServiceLogger.java | 7 +
...pleToDataSetRelatedEntitiesTranslator.java | 101 ++++++++++++++
.../generic/server/api/v1/Translator.java | 14 ++
.../api/v1/IGeneralInformationService.java | 10 ++
.../generic/shared/api/v1/dto/DataSet.java | 114 +++++++++++++++
.../generic/shared/api/v1/dto/Sample.java | 132 ++++++++++++++++--
.../api/v1/GeneralInformationServiceTest.java | 82 ++++++++++-
...oDataSetRelatedEntitiesTranslatorTest.java | 103 ++++++++++++++
.../generic/shared/api/v1/dto/SampleTest.java | 47 ++++++-
10 files changed, 617 insertions(+), 13 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslatorTest.java
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 25028d513e7..e68a302b864 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
@@ -36,12 +36,15 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
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;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
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.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
@@ -224,4 +227,21 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
return samples;
}
+
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples)
+ {
+ checkSession(sessionToken);
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType> sampleTypes =
+ commonServer.listSampleTypes(sessionToken);
+ SampleToDataSetRelatedEntitiesTranslator translator =
+ new SampleToDataSetRelatedEntitiesTranslator(sampleTypes, samples);
+ DataSetRelatedEntities dsre = translator.convertToDataSetRelatedEntities();
+ List<ExternalData> externalData = commonServer.listRelatedDataSets(sessionToken, dsre);
+ ArrayList<DataSet> dataSets = new ArrayList<DataSet>(externalData.size());
+ for (ExternalData externalDatum : externalData)
+ {
+ dataSets.add(Translator.translate(externalDatum));
+ }
+ return dataSets;
+ }
}
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 30389894a13..2582501e1ac 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
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -76,4 +77,10 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
return null;
}
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples)
+ {
+ logAccess(sessionToken, "list-data-sets", "SAMPLES(%s)", samples);
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
new file mode 100644
index 00000000000..bbe5246400e
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslator.java
@@ -0,0 +1,101 @@
+/*
+ * Copyright 2010 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.api.v1;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.BasicEntityInformationHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+
+/**
+ * A class that converts {@link Sample} objects to {@link DataSetRelatedEntities} objects.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class SampleToDataSetRelatedEntitiesTranslator
+{
+ // A map from sample type Id to sample type.
+ private final HashMap<Long, SampleType> sampleTypesMap;
+
+ private final List<Sample> samples;
+
+ private final ArrayList<BasicEntityInformationHolder> entityInformationHolders;
+
+ /**
+ * Creates a translator from public {@Sample} objects to the internal
+ * {@link DataSetRelatedEntities} objects.
+ * <p>
+ * A list of sample types known to the DB must be provided because Sample knows only the code of
+ * the SampleType.
+ *
+ * @param sampleTypes A list of SampleTypes known to the DB.
+ * @param samples The samples to convert.
+ */
+ public SampleToDataSetRelatedEntitiesTranslator(List<SampleType> sampleTypes,
+ List<Sample> samples)
+ {
+ this.sampleTypesMap = convertSampleTypesListToMap(sampleTypes);
+ this.samples = samples;
+ entityInformationHolders = new ArrayList<BasicEntityInformationHolder>(samples.size());
+ }
+
+ private static HashMap<Long, SampleType> convertSampleTypesListToMap(
+ List<SampleType> sampleTypes)
+ {
+ HashMap<Long, SampleType> map = new HashMap<Long, SampleType>(sampleTypes.size());
+
+ for (SampleType sampleType : sampleTypes)
+ {
+ map.put(sampleType.getId(), sampleType);
+ }
+
+ return map;
+ }
+
+ public DataSetRelatedEntities convertToDataSetRelatedEntities()
+ {
+ for (Sample sample : samples)
+ {
+ BasicEntityInformationHolder holderOrNull =
+ tryConvertSampleToEntityInformationHolder(sample);
+ if (null != holderOrNull)
+ {
+ entityInformationHolders.add(holderOrNull);
+ }
+ }
+ return new DataSetRelatedEntities(entityInformationHolders);
+ }
+
+ private BasicEntityInformationHolder tryConvertSampleToEntityInformationHolder(Sample sample)
+ {
+ EntityType entityType = sampleTypesMap.get(sample.getSampleTypeId());
+ if (null == entityType)
+ {
+ return null;
+ }
+ BasicEntityInformationHolder holder =
+ new BasicEntityInformationHolder(EntityKind.SAMPLE, entityType, sample.getCode(),
+ sample.getId());
+ return holder;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
index cbf4d4e77a4..101a4070368 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
@@ -16,9 +16,12 @@
package ch.systemsx.cisd.openbis.generic.server.api.v1;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleLevel;
@@ -40,11 +43,22 @@ class Translator
static Sample translate(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample privateSample)
{
SampleInitializer initializer = new SampleInitializer();
+ initializer.setId(privateSample.getId());
+ initializer.setCode(privateSample.getCode());
initializer.setIdentifier(privateSample.getIdentifier());
+ initializer.setSampleTypeId(privateSample.getSampleType().getId());
+ initializer.setSampleTypeCode(privateSample.getSampleType().getCode());
return new Sample(initializer);
}
private Translator()
{
}
+
+ public static DataSet translate(ExternalData externalDatum)
+ {
+ DataSetInitializer initializer = new DataSetInitializer();
+ initializer.setCode(externalDatum.getCode());
+ return new DataSet(initializer);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
index 15ce9594e5c..adf5228c035 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
@@ -23,6 +23,7 @@ import java.util.Set;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -90,4 +91,13 @@ public interface IGeneralInformationService extends IRpcService
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public List<Sample> searchForSamples(String sessionToken, SearchCriteria searchCriteria);
+ /**
+ * Return all data sets attached to the given samples.
+ *
+ * @param samples The samples for which we return attached data sets.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
new file mode 100644
index 00000000000..06dbb657c1a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
@@ -0,0 +1,114 @@
+/*
+ * Copyright 2010 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.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.commons.lang.builder.ToStringStyle;
+
+/**
+ * Immutable value object representing a data set.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public final class DataSet implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private final String code;
+
+ /**
+ * Class used to initialize a new data set instance. Necessary since all the fields of a DataSet
+ * are final.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ public static final class DataSetInitializer
+ {
+ private String code;
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+ }
+
+ /**
+ * Creates a new instance with the provided initializer
+ *
+ * @throws IllegalArgumentException if some of the required information is not provided.
+ */
+ public DataSet(DataSetInitializer initializer)
+ {
+ String id = initializer.getCode();
+ if (id == null || id.length() == 0)
+ {
+ throw new IllegalArgumentException("Unspecified code.");
+ }
+ this.code = id;
+ }
+
+ /**
+ * Returns the sample code;
+ */
+ public String getCode()
+ {
+ return code;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof DataSet == false)
+ {
+ return false;
+ }
+
+ EqualsBuilder builder = new EqualsBuilder();
+ DataSet other = (DataSet) obj;
+ builder.append(getCode(), other.getCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getCode());
+ return builder.toHashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
+ builder.append(getCode());
+ return builder.toString();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
index 87d6444f0f3..dfc8bd8d3ec 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
@@ -32,18 +32,47 @@ public final class Sample implements Serializable
{
private static final long serialVersionUID = 1L;
- private final String identifier;
-
/**
* Class used to initialize a new sample instance. Necessary since all the fields of a sample
* are final.
+ * <p>
+ * All of the properties must be filled (non-null) before being used to initialize a Sample,
+ * otherwise the Sample constructor will throw an exception.
*
* @author Chandrasekhar Ramakrishnan
*/
public static final class SampleInitializer
{
+ private Long id;
+
+ private String code;
+
private String identifier;
+ private Long sampleTypeId;
+
+ private String sampleTypeCode;
+
+ public void setId(Long id)
+ {
+ this.id = id;
+ }
+
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
public String getIdentifier()
{
return identifier;
@@ -53,8 +82,38 @@ public final class Sample implements Serializable
{
this.identifier = identifier;
}
+
+ public void setSampleTypeId(Long sampleTypeId)
+ {
+ this.sampleTypeId = sampleTypeId;
+ }
+
+ public Long getSampleTypeId()
+ {
+ return sampleTypeId;
+ }
+
+ public void setSampleTypeCode(String sampleTypeCode)
+ {
+ this.sampleTypeCode = sampleTypeCode;
+ }
+
+ public String getSampleTypeCode()
+ {
+ return sampleTypeCode;
+ }
}
+ private final Long id;
+
+ private final String code;
+
+ private final String identifier;
+
+ private final Long sampleTypeId;
+
+ private final String sampleTypeCode;
+
/**
* Creates a new instance with the provided initializer
*
@@ -62,12 +121,52 @@ public final class Sample implements Serializable
*/
public Sample(SampleInitializer initializer)
{
- String id = initializer.getIdentifier();
- if (id == null || id.length() == 0)
+ checkValidLong(initializer.getId(), "Unspecified id.");
+ this.id = initializer.getId();
+
+ checkValidString(initializer.getCode(), "Unspecified code.");
+ this.code = initializer.getCode();
+
+ checkValidString(initializer.getIdentifier(), "Unspecified identifier.");
+ this.identifier = initializer.getIdentifier();
+
+ checkValidLong(initializer.getSampleTypeId(), "Unspecified sample type id.");
+ this.sampleTypeId = initializer.getSampleTypeId();
+
+ checkValidString(initializer.getSampleTypeCode(), "Unspecified sample type code.");
+ this.sampleTypeCode = initializer.getSampleTypeCode();
+ }
+
+ private void checkValidString(String string, String message) throws IllegalArgumentException
+ {
+ if (string == null || string.length() == 0)
{
- throw new IllegalArgumentException("Unspecified identifier.");
+ throw new IllegalArgumentException(message);
}
- this.identifier = id;
+ }
+
+ private void checkValidLong(Long longValue, String message) throws IllegalArgumentException
+ {
+ if (longValue == null || longValue == 0)
+ {
+ throw new IllegalArgumentException(message);
+ }
+ }
+
+ /**
+ * Returns the sample id.
+ */
+ public Long getId()
+ {
+ return id;
+ }
+
+ /**
+ * Returns the sample code.
+ */
+ public String getCode()
+ {
+ return code;
}
/**
@@ -78,6 +177,22 @@ public final class Sample implements Serializable
return identifier;
}
+ /**
+ * Returns the sample type id.
+ */
+ public Long getSampleTypeId()
+ {
+ return sampleTypeId;
+ }
+
+ /**
+ * Returns the sample type code.
+ */
+ public String getSampleTypeCode()
+ {
+ return sampleTypeCode;
+ }
+
@Override
public boolean equals(Object obj)
{
@@ -92,7 +207,7 @@ public final class Sample implements Serializable
EqualsBuilder builder = new EqualsBuilder();
Sample other = (Sample) obj;
- builder.append(getIdentifier(), other.getIdentifier());
+ builder.append(getId(), other.getId());
return builder.isEquals();
}
@@ -100,7 +215,7 @@ public final class Sample implements Serializable
public int hashCode()
{
HashCodeBuilder builder = new HashCodeBuilder();
- builder.append(getIdentifier());
+ builder.append(getId());
return builder.toHashCode();
}
@@ -109,6 +224,7 @@ public final class Sample implements Serializable
{
ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
builder.append(getIdentifier());
+ builder.append(getSampleTypeCode());
return builder.toString();
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
index f78db9631c3..1fd96312e35 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
@@ -32,14 +32,18 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
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;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -180,6 +184,16 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
public void testSearchForSamples()
{
prepareGetSession();
+ prepareSearchForSamples();
+ List<Sample> result = service.searchForSamples(SESSION_TOKEN, createSearchCriteria());
+ assertEquals(1, result.size());
+ Sample resultSample = result.get(0);
+ assertEquals("/space/code", resultSample.getIdentifier());
+ context.assertIsSatisfied();
+ }
+
+ private void prepareSearchForSamples()
+ {
context.checking(new Expectations()
{
{
@@ -187,14 +201,76 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
with(any(DetailedSearchCriteria.class)));
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample returnSample =
new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
+ SampleType returnSampleType = new SampleType();
+ returnSample.setId(new Long(1));
+ returnSample.setCode("code");
returnSample.setIdentifier("/space/code");
+ returnSampleType.setId(new Long(1));
+ returnSampleType.setCode("sample-type");
+ returnSample.setSampleType(returnSampleType);
will(returnValue(Collections.singletonList(returnSample)));
}
});
- List<Sample> result = service.searchForSamples(SESSION_TOKEN, createSearchCriteria());
+ }
+
+ @Test
+ public void testListDataSets()
+ {
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(commonServer).listSampleTypes(SESSION_TOKEN);
+ SampleType returnSampleType = new SampleType();
+ returnSampleType.setId(new Long(1));
+ returnSampleType.setCode("sample-type");
+ will(returnValue(Collections.singletonList(returnSampleType)));
+
+ one(commonServer).listRelatedDataSets(with(SESSION_TOKEN),
+ with(any(DataSetRelatedEntities.class)));
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData returnData =
+ new ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData();
+ returnData.setCode("ds-code");
+ will(returnValue(Collections.singletonList(returnData)));
+ }
+ });
+
+ SampleInitializer initializer = new SampleInitializer();
+ initializer.setId(new Long(1));
+ initializer.setCode("code");
+ initializer.setIdentifier("/space/code");
+ initializer.setSampleTypeId(new Long(1));
+ initializer.setSampleTypeCode("sample-type");
+ Sample owner = new Sample(initializer);
+ List<DataSet> result =
+ service.listDataSets(SESSION_TOKEN, Collections.singletonList(owner));
assertEquals(1, result.size());
- Sample resultSample = result.get(0);
- assertEquals("/space/code", resultSample.getIdentifier());
+ DataSet resultDataSet = result.get(0);
+ assertEquals("ds-code", resultDataSet.getCode());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testListDataSetsWithEmptySampleList()
+ {
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(commonServer).listSampleTypes(SESSION_TOKEN);
+ SampleType returnSampleType = new SampleType();
+ returnSampleType.setId(new Long(1));
+ returnSampleType.setCode("sample-type");
+ will(returnValue(Collections.singletonList(returnSampleType)));
+
+ one(commonServer).listRelatedDataSets(with(SESSION_TOKEN),
+ with(any(DataSetRelatedEntities.class)));
+ will(returnValue(new ArrayList<ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData>()));
+ }
+ });
+ ArrayList<Sample> samples = new ArrayList<Sample>();
+ List<DataSet> result = service.listDataSets(SESSION_TOKEN, samples);
+ assertEquals(0, result.size());
context.assertIsSatisfied();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslatorTest.java
new file mode 100644
index 00000000000..8be49521105
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/SampleToDataSetRelatedEntitiesTranslatorTest.java
@@ -0,0 +1,103 @@
+/*
+; * Copyright 2010 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.api.v1;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SampleToDataSetRelatedEntitiesTranslatorTest extends AssertJUnit
+{
+ private SampleToDataSetRelatedEntitiesTranslator translator;
+
+ private static final Long SAMPLE_ID = new Long(1);
+
+ private static final String SAMPLE_CODE = "sample-code";
+
+ private static final String SAMPLE_IDENTIFIER = "/space/sample-code";
+
+ private static final Long SAMPLE_TYPE_ID = new Long(1);
+
+ private static final String SAMPLE_TYPE_CODE = "sample-type";
+
+ @BeforeMethod
+ public void setUp()
+ {
+ ArrayList<SampleType> sampleTypes = createSampleTypes();
+ ArrayList<Sample> samples = createSamples();
+ translator = new SampleToDataSetRelatedEntitiesTranslator(sampleTypes, samples);
+ }
+
+ private ArrayList<Sample> createSamples()
+ {
+ ArrayList<Sample> samples = new ArrayList<Sample>();
+ SampleInitializer initializer = new SampleInitializer();
+ initializer.setId(SAMPLE_ID);
+ initializer.setCode(SAMPLE_CODE);
+ initializer.setIdentifier(SAMPLE_IDENTIFIER);
+ initializer.setSampleTypeId(SAMPLE_TYPE_ID);
+ initializer.setSampleTypeCode(SAMPLE_TYPE_CODE);
+ Sample sample = new Sample(initializer);
+ samples.add(sample);
+ return samples;
+ }
+
+ private ArrayList<SampleType> createSampleTypes()
+ {
+ ArrayList<SampleType> sampleTypes = new ArrayList<SampleType>();
+ SampleType sampleType = new SampleType();
+ sampleType.setId(new Long(1));
+ sampleType.setCode("SAMPLE_TYPE");
+ sampleTypes.add(sampleType);
+ return sampleTypes;
+ }
+
+ @Test
+ public void testTranslator()
+ {
+ DataSetRelatedEntities dsre = translator.convertToDataSetRelatedEntities();
+ assertNotNull(dsre);
+ List<? extends IEntityInformationHolder> entities = dsre.getEntities();
+ assertEquals(1, entities.size());
+ }
+
+ @Test
+ public void testTranslatorWithEmptySampleTypes()
+ {
+ ArrayList<SampleType> sampleTypes = new ArrayList<SampleType>();
+ ArrayList<Sample> samples = createSamples();
+ SampleToDataSetRelatedEntitiesTranslator myTranslator =
+ new SampleToDataSetRelatedEntitiesTranslator(sampleTypes, samples);
+
+ DataSetRelatedEntities dsre = myTranslator.convertToDataSetRelatedEntities();
+ assertNotNull(dsre);
+ List<? extends IEntityInformationHolder> entities = dsre.getEntities();
+ assertEquals(0, entities.size());
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
index 978d1450aee..4676bc9eef1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleTest.java
@@ -27,33 +27,76 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializ
*/
public class SampleTest extends AssertJUnit
{
+ private static final Long SAMPLE_ID = new Long(1);
+
+ private static final String SAMPLE_CODE = "sample-code";
+
private static final String SAMPLE_IDENTIFIER = "/space/sample-code";
+ private static final Long SAMPLE_TYPE_ID = new Long(1);
+
+ private static final String SAMPLE_TYPE_CODE = "sample-type";
+
private Sample sample;
@BeforeMethod
public void setUp()
{
SampleInitializer initializer = new SampleInitializer();
+ initializer.setId(SAMPLE_ID);
+ initializer.setCode(SAMPLE_CODE);
initializer.setIdentifier(SAMPLE_IDENTIFIER);
+ initializer.setSampleTypeId(SAMPLE_TYPE_ID);
+ initializer.setSampleTypeCode(SAMPLE_TYPE_CODE);
sample = new Sample(initializer);
}
+ @Test(expectedExceptions =
+ { IllegalArgumentException.class })
+ public void testInitialization()
+ {
+ SampleInitializer initializer = new SampleInitializer();
+ initializer.setIdentifier(SAMPLE_IDENTIFIER);
+ new Sample(initializer);
+ }
+
@Test
public void testEquals()
{
SampleInitializer initializer = new SampleInitializer();
+ initializer.setId(SAMPLE_ID);
+ initializer.setCode(SAMPLE_CODE);
initializer.setIdentifier(SAMPLE_IDENTIFIER);
+ initializer.setSampleTypeId(SAMPLE_TYPE_ID);
+ initializer.setSampleTypeCode(SAMPLE_TYPE_CODE);
Sample mySample = new Sample(initializer);
+ assertTrue("Samples with the same id should be equal.", sample.equals(mySample));
+ assertEquals(sample.hashCode(), mySample.hashCode());
- assertTrue(sample.equals(mySample));
+ initializer = new SampleInitializer();
+ initializer.setId(SAMPLE_ID);
+ initializer.setCode("different-code");
+ initializer.setIdentifier("/a/different-identifier");
+ initializer.setSampleTypeId(new Long(2));
+ initializer.setSampleTypeCode("new-code");
+ mySample = new Sample(initializer);
+ assertTrue("Samples with the same id should be equal.", sample.equals(mySample));
assertEquals(sample.hashCode(), mySample.hashCode());
+
+ initializer = new SampleInitializer();
+ initializer.setId(new Long(2));
+ initializer.setCode(SAMPLE_CODE);
+ initializer.setIdentifier(SAMPLE_IDENTIFIER);
+ initializer.setSampleTypeId(SAMPLE_TYPE_ID);
+ initializer.setSampleTypeCode(SAMPLE_TYPE_CODE);
+ mySample = new Sample(initializer);
+ assertFalse("Samples with the different ids should not be equal.", sample.equals(mySample));
}
@Test
public void testToString()
{
String stringRepresentation = sample.toString();
- assertEquals("Sample[/space/sample-code]", stringRepresentation);
+ assertEquals("Sample[/space/sample-code,sample-type]", stringRepresentation);
}
}
--
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