diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index cf175c2a91fe6f32afd7e461773f9b85195246e2..95c32d655760c742eab3610530b145610eba6296 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -282,9 +282,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
break;
case SAMPLE:
SampleIdentifier sampleId = trySampleIdentifier();
-
- dataSetInfo.setSampleCode(sampleId.getSampleCode());
- dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setSampleIdentifier(sampleId);
break;
case DATA_SET:
String dataSetCode = tryGetDataSetCode();
@@ -735,9 +733,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
break;
case SAMPLE:
SampleIdentifier sampleId = trySampleIdentifier();
-
- dataSetInfo.setSampleCode(sampleId.getSampleCode());
- dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setSampleIdentifier(sampleId);
break;
case DATA_SET:
String dataSetCode = tryGetDataSetCode();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
index ed03cf3d54231437bf2686a3a81c51f7bfc1d17b..ef3d528e22e8b9cbf0b7dc66cac0cb18c78ad80a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetTopLevelDataSetHandler.java
@@ -190,9 +190,7 @@ class PutDataSetTopLevelDataSetHandler
break;
case SAMPLE:
SampleIdentifier sampleId = trySampleIdentifier();
-
- dataSetInfo.setSampleCode(sampleId.getSampleCode());
- dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setSampleIdentifier(sampleId);
break;
case DATA_SET:
String dataSetCode = tryGetDataSetCode();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
index 95a392bb0b271d44c0938c0c6c1fcc9e4c6dd68e..aaac89863745b5c26cc83e6cf8aaf82048e82a2a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/cifex/CifexDataSetInfoExtractor.java
@@ -78,12 +78,7 @@ public class CifexDataSetInfoExtractor implements IDataSetInfoExtractor
SampleIdentifier sampleIdentifierOrNull = tryGetSampleIdentifier(info);
if (sampleIdentifierOrNull != null)
{
- dataSetInformation.setSampleCode(sampleIdentifierOrNull.getSampleCode());
- if (sampleIdentifierOrNull.isSpaceLevel())
- {
- dataSetInformation.setSpaceCode(sampleIdentifierOrNull.getSpaceLevel()
- .getSpaceCode());
- }
+ dataSetInformation.setSampleIdentifier(sampleIdentifierOrNull);
} else
{
ExperimentIdentifier experimentIdentifier =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
index 3f1c33ce297f02a604961d0f952fbe8fe34304a6..9dc41318633f751bc7645f9d50163289fb11febf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
@@ -413,14 +413,23 @@ public abstract class AbstractTransactionState<T extends DataSetInformation>
{
return false;
}
+ if (sampleIdentifier.isProjectLevel())
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project projectDTO = sampleDTO.getProject();
+ if (projectDTO == null)
+ {
+ return false;
+ }
+ ProjectIdentifier project = sampleIdentifier.getProjectLevel();
+ return project.getProjectCode().equals(projectDTO.getCode())
+ && project.getSpaceCode().equals(projectDTO.getSpace().getCode());
+ }
if (sampleIdentifier.isSpaceLevel())
{
return sampleIdentifier.getSpaceLevel().getSpaceCode()
.equals(sampleDTO.getSpace().getCode());
}
- {
- return sampleDTO.getSpace() == null;
- }
+ return sampleDTO.getSpace() == null;
}
public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSet.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSet.java
index 5a02dd5d75c1aa793f3388f1201e0087017e6629..8bc2c309b84df8f88661d833749d2c8a533bf489 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSet.java
@@ -37,7 +37,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCode
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -165,13 +164,7 @@ public class DataSet<T extends DataSetInformation> extends AbstractDataSetImmuta
SampleImmutable sample = (SampleImmutable) sampleOrNull;
Sample sampleDTO = sample.getSample();
- dataSetInformation.setSample(sampleDTO);
- dataSetInformation.setSampleCode(sampleDTO.getCode());
- Space space = sampleDTO.getSpace();
- if (null != space)
- {
- dataSetInformation.setSpaceCode(space.getCode());
- }
+ dataSetInformation.setSampleIdentifier(sampleDTO.getIdentifier());
if (sampleDTO.getExperiment() != null)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/Sample.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/Sample.java
index 4e4b2a6dc9bfe00e5e8885d06d2281ebd181ee74..30dd74af380e9fe48ec4b331391252b375dfd66d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/Sample.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/Sample.java
@@ -26,9 +26,11 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentIm
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -58,7 +60,17 @@ public class Sample extends SampleImmutable implements ISample
sample.setCode(sampleIdentifier.getSampleCode());
String sampleSubCode = sampleIdentifier.getSampleSubCode();
sample.setSubCode(sampleSubCode);
- if (sampleIdentifier.isSpaceLevel())
+ if (sampleIdentifier.isProjectLevel())
+ {
+ ProjectIdentifier projectLevel = sampleIdentifier.getProjectLevel();
+ Space space = new Space();
+ space.setCode(projectLevel.getSpaceCode());
+ Project project = new Project();
+ project.setSpace(space);
+ project.setCode(projectLevel.getProjectCode());
+ sample.setSpace(space);
+ sample.setProject(project);
+ } else if (sampleIdentifier.isSpaceLevel())
{
Space space = new Space();
SpaceIdentifier spaceLevel = sampleIdentifier.getSpaceLevel();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v1/AbstractDataSetRegistrationDetailsFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v1/AbstractDataSetRegistrationDetailsFactory.java
index 7aa93c512c3d3c856787d4f309073382a416db34..9a1774f9f05299d32ba5393875c2cad6943dd719 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v1/AbstractDataSetRegistrationDetailsFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v1/AbstractDataSetRegistrationDetailsFactory.java
@@ -94,8 +94,7 @@ public abstract class AbstractDataSetRegistrationDetailsFactory<T extends DataSe
SampleIdentifier sampleId = userProvidedDataSetInformationOrNull.getSampleIdentifier();
if (null != sampleId)
{
- dataSetInfo.setSampleCode(sampleId.getSampleCode());
- dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setSampleIdentifier(sampleId);
}
if (null != userProvidedDataSetInformationOrNull.tryToGetSample())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v2/AbstractDataSetRegistrationDetailsFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v2/AbstractDataSetRegistrationDetailsFactory.java
index 38739c70c7fd5569ee33b5f037728321f1ae301a..7a2142efad063c4ace4bb3688cb66d104f403e7b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v2/AbstractDataSetRegistrationDetailsFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/v2/AbstractDataSetRegistrationDetailsFactory.java
@@ -94,8 +94,7 @@ public abstract class AbstractDataSetRegistrationDetailsFactory<T extends DataSe
SampleIdentifier sampleId = userProvidedDataSetInformationOrNull.getSampleIdentifier();
if (null != sampleId)
{
- dataSetInfo.setSampleCode(sampleId.getSampleCode());
- dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setSampleIdentifier(sampleId);
}
if (null != userProvidedDataSetInformationOrNull.tryToGetSample())
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
index b4c57d4f0c1ba23e84d9cb4e800dea59e48d4852..db67fc407cdc4318e6214c8e1f5e03bc3a629f94 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractDropboxProcessingPlugin.java
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -200,23 +201,35 @@ abstract public class AbstractDropboxProcessingPlugin extends AbstractDatastoreP
private DataSetInformation createDatasetInfo(DatasetDescription dataset)
{
- DataSetInformation datasetInfo = new DataSetInformation();
String datasetTypeCode = dataset.getDataSetTypeCode();
+ String spaceCode = dataset.getSpaceCode();
+ String projectCode = dataset.getProjectCode();
+ String sampleCode = dataset.getSampleCode();
+ String experimentCode = dataset.getExperimentCode();
+ DataSetInformation datasetInfo = new DataSetInformation();
datasetInfo.setDataSetType(new DataSetType(datasetTypeCode));
- datasetInfo.setSampleCode(dataset.getSampleCode());
- datasetInfo.setSpaceCode(dataset.getSpaceCode());
+ datasetInfo.setSampleCode(sampleCode);
+ datasetInfo.setProjectCode(projectCode);
+ datasetInfo.setSpaceCode(spaceCode);
datasetInfo.setDataSetCode(dataset.getDataSetCode());
- if (dataset.getExperimentCode() != null)
+ if (experimentCode != null)
{
- ExperimentIdentifier expIdent =
- new ExperimentIdentifier(dataset.getSpaceCode(), dataset.getProjectCode(),
- dataset.getExperimentCode());
+ ExperimentIdentifier expIdent = new ExperimentIdentifier(spaceCode, projectCode, experimentCode);
datasetInfo.setExperimentIdentifier(expIdent);
}
- if (dataset.getSampleCode() != null)
+ if (sampleCode != null)
{
- SpaceIdentifier spaceIdentifier = new SpaceIdentifier(dataset.getSpaceCode());
- datasetInfo.setSampleIdentifier(new SampleIdentifier(spaceIdentifier, dataset.getSampleCode()));
+ SampleIdentifier sampleIdentifier;
+ if (projectCode != null)
+ {
+ ProjectIdentifier projectIdentifier = new ProjectIdentifier(spaceCode, projectCode);
+ sampleIdentifier = new SampleIdentifier(projectIdentifier, sampleCode);
+ } else
+ {
+ SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
+ sampleIdentifier = new SampleIdentifier(spaceIdentifier, sampleCode);
+ }
+ datasetInfo.setSampleIdentifier(sampleIdentifier);
}
return datasetInfo;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
index 61de7ba18d14689dbaf602361a02a67b96637290..cfbe68c1618380cfe407d63dcf348b137a8b8e1f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/dto/DataSetInformation.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExtractableData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -67,11 +68,8 @@ public class DataSetInformation implements Serializable
*/
private String instanceUUID;
- /**
- * The database instance code.
- */
- private String instanceCode;
-
+ private String projectCode;
+
private String spaceCode;
/** An object that uniquely identifies the experiment. Can be <code>null</code>. */
@@ -252,6 +250,10 @@ public class DataSetInformation implements Serializable
{
return null;
}
+ if (projectCode != null)
+ {
+ return new SampleIdentifier(new ProjectIdentifier(spaceCode, projectCode), sampleCode);
+ }
if (spaceCode == null)
{
return new SampleIdentifier(sampleCode);
@@ -263,13 +265,23 @@ public class DataSetInformation implements Serializable
/**
* Sets the sample identifier.
*/
- public final void setSampleIdentifier(SampleIdentifier sampleIdentifier)
+ public final void setSampleIdentifier(SampleIdentifier sampleIdentifierOrNull)
{
- setSampleCode(sampleIdentifier.getSampleCode());
- final SpaceIdentifier spaceLevel = sampleIdentifier.getSpaceLevel();
- if (spaceLevel != null)
+ if (sampleIdentifierOrNull != null)
{
- setSpaceCode(spaceLevel.getSpaceCode());
+ setSampleCode(sampleIdentifierOrNull.getSampleCode());
+ if (sampleIdentifierOrNull.isProjectLevel())
+ {
+ setProjectCode(sampleIdentifierOrNull.getProjectLevel().getProjectCode());
+ setSpaceCode(sampleIdentifierOrNull.getProjectLevel().getSpaceCode());
+ } else
+ {
+ final SpaceIdentifier spaceLevel = sampleIdentifierOrNull.getSpaceLevel();
+ if (spaceLevel != null)
+ {
+ setSpaceCode(spaceLevel.getSpaceCode());
+ }
+ }
}
}
@@ -348,6 +360,16 @@ public class DataSetInformation implements Serializable
extractableData.setParentDataSetCodes(parentDataSetCodes);
}
+ public String getProjectCode()
+ {
+ return projectCode;
+ }
+
+ public void setProjectCode(String projectCode)
+ {
+ this.projectCode = projectCode;
+ }
+
public final void setSpaceCode(final String spaceCode)
{
this.spaceCode = spaceCode;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleGenericBusinessRules.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleGenericBusinessRules.java
index 47f507f774e48936311f8e2a0135752d8b0902a1..ed5bb218382c20c4718eb52fe2d5ce0bed303aa1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleGenericBusinessRules.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleGenericBusinessRules.java
@@ -45,8 +45,9 @@ public class SampleGenericBusinessRules
{
if (child.getSpace() == null)
{
+ String kind = parent.getProject() == null ? "space" : "project";
throwUserFailureException("The database instance sample '%s' "
- + "can not be %s the space sample '%s'.", child, parent, childRelationName);
+ + "can not be %s the " + kind + " sample '%s'.", child, parent, childRelationName);
}
}
}
@@ -60,14 +61,15 @@ public class SampleGenericBusinessRules
// new identifier of a parent is needed for comparison
SampleIdentifier parentId = IdentifierHelper.createSampleIdentifier(parent);
- if (parentId.isSpaceLevel())
+ if (parentId.isSpaceLevel() || parentId.isProjectLevel())
{
+ String kind = parentId.isProjectLevel() ? "project" : "sample";
for (SamplePE child : children)
{
SampleIdentifier childId = child.getSampleIdentifier();
if (childId.isDatabaseInstanceLevel())
{
- throwUserFailureException("Sample '%s' can not be a space sample because of "
+ throwUserFailureException("Sample '%s' can not be a space " + kind + " because of "
+ "a %s database instance sample '%s'.", parent, child,
childRelationName);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProvider.java
index 7c353905158da9e12a9d834d60642169dd2de058..3168a99c49bcca42dd92dea1daddf2b712f0540d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProvider.java
@@ -29,9 +29,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifierHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.EntityLinkElementTranslator;
@@ -117,6 +119,16 @@ public class EntityInformationProvider implements IEntityInformationProvider
return space;
}
+
+ private ProjectPE tryGetProjectByCode(String spaceCode, String projectCode)
+ {
+ ProjectPE project = daoFactory.getProjectDAO().tryFindProject(spaceCode, projectCode);
+ if (project == null)
+ {
+ throw new UserFailureException("Project /" + spaceCode + "/" + projectCode + " doesn't exist.");
+ }
+ return project;
+ }
@Override
public String getSamplePermId(String spaceCode, String sampleCode)
@@ -126,11 +138,27 @@ public class EntityInformationProvider implements IEntityInformationProvider
return (sample != null) ? sample.getPermId() : null;
}
+ @Override
+ public String getProjectSamplePermId(String spaceCode, String projectCode, String sampleCode)
+ {
+
+ ProjectPE project = tryGetProjectByCode(spaceCode, projectCode);
+ SamplePE sample = daoFactory.getSampleDAO().tryfindByCodeAndProject(sampleCode, project);
+ return (sample != null) ? sample.getPermId() : null;
+ }
+
@Override
public String getSamplePermId(String sampleIdentifier)
{
SampleIdentifier identifier = SampleIdentifierFactory.parse(sampleIdentifier);
String sampleCode = identifier.getSampleCode();
+ if (identifier.isProjectLevel())
+ {
+ ProjectIdentifier projectIdentifier = identifier.getProjectLevel();
+ String spaceCode = projectIdentifier.getSpaceCode();
+ String projectCode = projectIdentifier.getProjectCode();
+ return getProjectSamplePermId(spaceCode, projectCode, sampleCode);
+ }
if (identifier.isSpaceLevel())
{
String spaceCode = identifier.getSpaceLevel().getSpaceCode();
@@ -185,6 +213,19 @@ public class EntityInformationProvider implements IEntityInformationProvider
return getSamplesPermIds(sample.getParents());
}
+ @Override
+ public List<String> getProjectSampleParentPermIds(String spaceCode, String projectCode, String sampleCode)
+ {
+ ProjectPE project = tryGetProjectByCode(spaceCode, projectCode);
+ SamplePE sample = daoFactory.getSampleDAO().tryfindByCodeAndProject(sampleCode, project);
+ if (sample == null)
+ {
+ throw new UserFailureException("Sample /" + spaceCode + "/" + projectCode + "/"
+ + sampleCode + " doesn't exist.");
+ }
+ return getSamplesPermIds(sample.getParents());
+ }
+
@Override
public List<String> getSampleParentPermIds(String permId)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/SpaceIdentifierHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/SpaceIdentifierHelper.java
index f30db5b7979ecead93323ee87703477085c0326e..129c04a2bde15ad99d447db272d1104d203ec18a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/SpaceIdentifierHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/SpaceIdentifierHelper.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.util;
-import ch.systemsx.cisd.common.exceptions.InternalErr;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISpaceDAO;
@@ -24,15 +23,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.util.SpaceCodeHelper;
/**
* Some useful identifier methods on the <i>server</i> side.
- * <p>
- * This class is the only place which provides the correct way to resolve {@link DatabaseInstanceIdentifier} into a {@link DatabaseInstancePE}!
- * </p>
*
* @author Franz-Josef Elmer
*/
@@ -44,66 +39,6 @@ public final class SpaceIdentifierHelper
// Can not be instantiated.
}
- /**
- * Class which transforms identifiers to the canonical form. Normalized database identifier always has a code, never UUID. Normalized space
- * identifier has always space code, even when it is a home space. It also has normalized database identifier.
- */
- public static class SpaceIdentifierNormalizer
- {
- public static SpaceIdentifierNormalizer create(final IAuthorizationDAOFactory daoFactory,
- final String homeSpaceCodeOrNull)
- {
- return new SpaceIdentifierNormalizer(homeSpaceCodeOrNull);
- }
-
- private final String homeSpaceCodeOrNull;
-
- private SpaceIdentifierNormalizer(final String homeSpaceCodeOrNull)
- {
- this.homeSpaceCodeOrNull = homeSpaceCodeOrNull;
- }
-
- public final SpaceIdentifier normalize(final SpaceIdentifier identifier)
- {
- return SpaceIdentifierHelper.normalize(identifier, homeSpaceCodeOrNull);
- }
-
- public final SampleIdentifier normalize(final SampleIdentifier identifier)
- {
- return SpaceIdentifierHelper.normalize(identifier, homeSpaceCodeOrNull);
- }
- }
-
- /** Transforms given space identifier to the canonical form. */
- private final static SpaceIdentifier normalize(final SpaceIdentifier spaceIdentifier,
- final String homeSpaceCodeOrNull)
- {
- String spaceCode = spaceIdentifier.getSpaceCode();
- if (spaceCode == null)
- {
- spaceCode = homeSpaceCodeOrNull;
- }
- return new SpaceIdentifier(spaceCode.toUpperCase());
- }
-
- /** Transforms given sample identifier to the canonical form. */
- private final static SampleIdentifier normalize(final SampleIdentifier sampleIdentifier,
- final String homeSpaceCodeOrNull)
- {
- if (sampleIdentifier.isDatabaseInstanceLevel())
- {
- return new SampleIdentifier(sampleIdentifier.getSampleCode());
- } else if (sampleIdentifier.isSpaceLevel())
- {
- final SpaceIdentifier spaceIdentifier =
- normalize(sampleIdentifier.getSpaceLevel(), homeSpaceCodeOrNull);
- return new SampleIdentifier(spaceIdentifier, sampleIdentifier.getSampleCode());
- } else
- {
- throw InternalErr.error(sampleIdentifier);
- }
- }
-
/** finds a space in the database for the given identifier */
public static final SpacePE tryGetSpace(final SpaceIdentifier spaceIdentifier,
final PersonPE person, final IAuthorizationDAOFactory daoFactory)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
index 161f675ac98407f5a6c1f555552c6ba099ee1548..90b0ebd361331d424d0160c64cd61546426f6aeb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/managed_property/api/IEntityInformationProvider.java
@@ -36,6 +36,11 @@ public interface IEntityInformationProvider
*/
String getSamplePermId(String spaceCode, String sampleCode);
+ /**
+ * @return permId of project sample specified by given space, project and code, <code>null</code> if such a sample doesn't exist
+ */
+ String getProjectSamplePermId(String spaceCode, String projectCode, String sampleCode);
+
/**
* @return permId of sample specified by given identifier, <code>null</code> if such a sample doesn't exist
*/
@@ -46,6 +51,11 @@ public interface IEntityInformationProvider
*/
List<String> getSampleParentPermIds(String spaceCode, String sampleCode);
+ /**
+ * @return list of permIds of parents of a project sample with given space, project and code
+ */
+ List<String> getProjectSampleParentPermIds(String spaceCode, String projectCode, String sampleCode);
+
/**
* @return list of permIds of parents of a sample with given permId
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
index 154b2df859e39637f7151a723462ea74ea3b50eb..d9b3c41c5c0e7055c36341055eae532aec4db26f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
@@ -125,6 +125,11 @@ public class DataSetTranslator
{
description.setSampleTypeCode(sampleType.getCode());
}
+ Project project = sample.getProject();
+ if (project != null)
+ {
+ description.setProjectCode(project.getCode());
+ }
Space space = sample.getSpace();
if (space != null)
{
@@ -465,6 +470,11 @@ public class DataSetTranslator
description.setSampleCode(sample.getCode());
description.setSampleIdentifier(sample.getIdentifier());
description.setSampleTypeCode(sample.getSampleType().getCode());
+ ProjectPE project = sample.getProject();
+ if (project != null)
+ {
+ description.setProjectCode(project.getCode());
+ }
description.setSpaceCode(sample.getSpace().getCode());
}
ExperimentPE experiment = dataSet.getExperiment();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/EntityExistenceChecker.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/EntityExistenceChecker.java
index 6f4fd657a58b08f5be145f86e00b77918ef9fd2c..3727c8901bf426c2e4696c92b213253d44adfe0a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/EntityExistenceChecker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/EntityExistenceChecker.java
@@ -24,6 +24,7 @@ import java.util.Set;
import java.util.TreeSet;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
@@ -45,6 +46,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -190,6 +192,19 @@ class EntityExistenceChecker
return sampleDAO.tryFindByCodeAndSpace(sampleCode,
spaceExistenceManager.tryGet(spaceLevel));
}
+ if (identifier.isProjectLevel())
+ {
+ ProjectIdentifier projectIdentifier = identifier.getProjectLevel();
+ IProjectDAO projectDAO = daoFactory.getProjectDAO();
+ String spaceCode = projectIdentifier.getSpaceCode();
+ String projectCode = projectIdentifier.getProjectCode();
+ ProjectPE project = projectDAO.tryFindProject(spaceCode, projectCode);
+ if (project == null)
+ {
+ return null;
+ }
+ return sampleDAO.tryfindByCodeAndProject(sampleCode, project);
+ }
return sampleDAO.tryFindByCodeAndDatabaseInstance(sampleCode);
}
};
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProviderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProviderTest.java
index 020226eaaa790b61c4b6074eb6480cd2d0f23895..962ff97e72dfe094732812cd48533b92de976aac 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProviderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/managed_property/EntityInformationProviderTest.java
@@ -27,7 +27,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.api.IEntityLinkElement;
import ch.systemsx.cisd.openbis.generic.shared.managed_property.structured.ElementFactory;
@@ -118,4 +120,108 @@ public class EntityInformationProviderTest extends AbstractBOTest
context.assertIsSatisfied();
}
+
+ @Test
+ public void testGetProjectSamplePermId()
+ {
+ final SamplePE sample = new SamplePE();
+ final ProjectPE project = new ProjectPE();
+ SpacePE space = new SpacePE();
+ space.setCode("S1");
+ project.setSpace(space);
+ project.setCode("P1");
+ sample.setProject(project);
+ sample.setCode("SAMP1");
+ sample.setPermId("123");
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDAO).tryFindProject("S1", "P1");
+ will(returnValue(project));
+
+ one(sampleDAO).tryfindByCodeAndProject("SAMP1", project);
+ will(returnValue(sample));
+ }
+ });
+
+ String permId = provider.getProjectSamplePermId("S1", "P1", "SAMP1");
+
+ assertEquals("123", permId);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testGetProjectSampleByIdentifier()
+ {
+ final SamplePE sample = new SamplePE();
+ final ProjectPE project = new ProjectPE();
+ SpacePE space = new SpacePE();
+ space.setCode("S1");
+ project.setSpace(space);
+ project.setCode("P1");
+ sample.setProject(project);
+ sample.setCode("SAMP1");
+ sample.setPermId("123");
+ context.checking(new Expectations()
+ {
+ {
+ one(projectDAO).tryFindProject("S1", "P1");
+ will(returnValue(project));
+
+ one(sampleDAO).tryfindByCodeAndProject("SAMP1", project);
+ will(returnValue(sample));
+ }
+ });
+
+ String permId = provider.getSamplePermId("/S1/P1/SAMP1");
+
+ assertEquals("123", permId);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testGetSpaceSampleByIdentifier()
+ {
+ final SamplePE sample = new SamplePE();
+ final SpacePE space = new SpacePE();
+ space.setCode("S1");
+ sample.setSpace(space);
+ sample.setCode("SAMP1");
+ sample.setPermId("123");
+ context.checking(new Expectations()
+ {
+ {
+ one(spaceDAO).tryFindSpaceByCode("S1");
+ will(returnValue(space));
+
+ one(sampleDAO).tryFindByCodeAndSpace("SAMP1", space);
+ will(returnValue(sample));
+ }
+ });
+
+ String permId = provider.getSamplePermId("/S1/SAMP1");
+
+ assertEquals("123", permId);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testGetSharedSampleByIdentifier()
+ {
+ final SamplePE sample = new SamplePE();
+ sample.setCode("SAMP1");
+ sample.setPermId("123");
+ context.checking(new Expectations()
+ {
+ {
+ one(sampleDAO).tryFindByCodeAndDatabaseInstance("SAMP1");
+ will(returnValue(sample));
+ }
+ });
+
+ String permId = provider.getSamplePermId("/SAMP1");
+
+ assertEquals("123", permId);
+ context.assertIsSatisfied();
+ }
}