From 6db40fc61a04924daf100c221b3380e8a9d1976a Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Sun, 24 Sep 2017 15:22:42 +0000
Subject: [PATCH] SSDM-5661 : AS V3 API : Support for semantic annotations -
create/get methods (JS tests still missing) - bugfixes
SVN: 38757
---
.../server/dssapi/v3/DataStoreServerApi.java | 58 +++++++++++++------
.../source/sql/postgresql/166/grants-166.sql | 2 +-
2 files changed, 42 insertions(+), 18 deletions(-)
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
index 57ddb1b8f21..f1d90764103 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
@@ -49,9 +49,11 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.IDataStoreId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.IEntityTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
+import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.UnsupportedObjectIdException;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.FullDataSetCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
@@ -92,6 +94,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvi
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.IQueryApiServer;
+
import net.lemnik.eodsql.QueryTool;
/**
@@ -356,31 +359,44 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
ownerType = DataSetOwnerType.EXPERIMENT;
owner = new NewDataSetDTO.DataSetOwner(ownerType, experimentIdentifier.toString());
}
- if(owner == null) {
+ if (owner == null)
+ {
throw new UserFailureException("A dataset needs either a Sample or Experiment as owner.");
}
IEntityTypeId typeId = dataSetCreation.getMetadataCreation().getTypeId();
-
+ String typeCode = null;
+
+ if (typeId != null)
+ {
+ if (typeId instanceof EntityTypePermId)
+ {
+ typeCode = ((EntityTypePermId) typeId).getPermId();
+ } else
+ {
+ throw new UnsupportedObjectIdException(typeId);
+ }
+ }
+
List<FileInfoDssDTO> fileInfos = FileInfoDssBuilder.getFileInfos(temporaryIncomingDir);
- NewDataSetDTO dataSet = new NewDataSetDTO(typeId.toString(), owner, null, fileInfos);
+ NewDataSetDTO dataSet = new NewDataSetDTO(typeCode, owner, null, fileInfos);
return dataSet;
}
-
+
private List<FullDataSetCreation> filterPhysicalDataSets(List<FullDataSetCreation> newDataSets)
{
return newDataSets
- .stream()
- .filter((dataSetCreation) -> dataSetCreation.getMetadataCreation().getPhysicalData() != null)
- .collect(Collectors.toList());
+ .stream()
+ .filter((dataSetCreation) -> dataSetCreation.getMetadataCreation().getPhysicalData() != null)
+ .collect(Collectors.toList());
}
private List<FullDataSetCreation> filterNonPhysicalDataSets(List<FullDataSetCreation> newDataSets)
{
return newDataSets
- .stream()
- .filter((dataSetCreation) -> dataSetCreation.getMetadataCreation().getPhysicalData() == null)
- .collect(Collectors.toList());
+ .stream()
+ .filter((dataSetCreation) -> dataSetCreation.getMetadataCreation().getPhysicalData() == null)
+ .collect(Collectors.toList());
}
@Override
@@ -442,29 +458,37 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
for (FullDataSetCreation dataSetCreation : newDataSets)
{
PutDataSetService putService =
- new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
+ new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
putService.setStoreDirectory(ServiceProvider.getConfigProvider().getStoreRoot());
NewDataSetDTO newDataset;
try
- { DataSetCreation metadataCreation = dataSetCreation.getMetadataCreation();
+ {
+ DataSetCreation metadataCreation = dataSetCreation.getMetadataCreation();
CreationId creationId = metadataCreation.getCreationId();
String dataSetTypeCodeNull = null;
IEntityTypeId typeId = metadataCreation.getTypeId();
- if(null != typeId) {
- dataSetTypeCodeNull = typeId.toString();
+ if (null != typeId)
+ {
+ if (typeId instanceof EntityTypePermId)
+ {
+ dataSetTypeCodeNull = ((EntityTypePermId) typeId).getPermId();
+ } else
+ {
+ throw new UnsupportedObjectIdException(typeId);
+ }
}
- File temporaryIncomingDir = putService.getTemporaryIncomingDir(dataSetTypeCodeNull, creationId.toString());
+ File temporaryIncomingDir = putService.getTemporaryIncomingDir(dataSetTypeCodeNull, creationId.toString());
newDataset = getNewDataSet(dataSetCreation, temporaryIncomingDir);
String code = dataSetCreation.getMetadataCreation().getCode();
putService.putDataSet(sessionToken, newDataset, creationId.toString(), code);
-
+
} catch (IOException e)
{
operationLog.error(e.getMessage());
}
}
}
-
+
private void injectDataStoreIdAndCodesIfNeeded(List<FullDataSetCreation> newDataSets)
{
String dataStoreCode = configProvider.getDataStoreCode();
diff --git a/openbis/source/sql/postgresql/166/grants-166.sql b/openbis/source/sql/postgresql/166/grants-166.sql
index 7d3b24b7bc5..8d81b1f5318 100644
--- a/openbis/source/sql/postgresql/166/grants-166.sql
+++ b/openbis/source/sql/postgresql/166/grants-166.sql
@@ -127,4 +127,4 @@ GRANT SELECT ON TABLE METAPROJECTS TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE METAPROJECT_ASSIGNMENTS_ALL TO GROUP OPENBIS_READONLY;
GRANT SELECT ON METAPROJECT_ASSIGNMENTS TO GROUP OPENBIS_READONLY;
GRANT SELECT ON TABLE OPERATION_EXECUTIONS TO GROUP OPENBIS_READONLY;
-GRANT SELECT ON TABLE ANNOTATIONS TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE SEMANTIC_ANNOTATIONS TO GROUP OPENBIS_READONLY;
--
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