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 f92dea95b818c2ba16fbd5e2df28f877d6f9d903..e435744da7e2377f81cc836aed0399f4538fa1cc 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
@@ -15,8 +15,6 @@
*/
package ch.ethz.sis.openbis.generic.server.dssapi.v3;
-import java.io.File;
-import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
@@ -28,17 +26,14 @@ import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.stream.Collectors;
import org.apache.commons.collections4.iterators.IteratorChain;
import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.CreationId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.ISearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchOperator;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
@@ -49,13 +44,9 @@ 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.dataset.create.UploadedDataSetCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.create.DataSetFileCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
@@ -64,14 +55,12 @@ import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.DataSetFilePermI
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.IDataSetFileId;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
import ch.ethz.sis.openbis.generic.server.dssapi.v3.download.DataSetFileDownloadInputStream;
+import ch.ethz.sis.openbis.generic.server.dssapi.v3.executor.ICreateUploadedDataSetExecutor;
import ch.ethz.sis.openbis.generic.server.dssapi.v3.pathinfo.PathInfoFeeder;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.IFreeSpaceProvider;
import ch.systemsx.cisd.common.filesystem.SimpleFreeSpaceProvider;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.etlserver.api.v1.PutDataSetService;
import ch.systemsx.cisd.etlserver.path.IPathsInfoDAO;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
@@ -83,13 +72,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.DssSessionAuthorizationHolder;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.PathInfoDataSourceProvider;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
@@ -109,12 +92,6 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
*/
public static final String INTERNAL_SERVICE_NAME = "data-store-server_INTERNAL";
- /**
- * Logger with {@link LogCategory#OPERATION} with name of the concrete class, needs to be static for our purpose.
- */
- protected static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- DataStoreServerApi.class);
-
public String DSS_SERVICE_NAME = "DSS Service";
@Autowired
@@ -123,6 +100,9 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
@Autowired
private IApplicationServerApi as;
+ @Autowired
+ private ICreateUploadedDataSetExecutor createUploadedDataSetExecutor;
+
/**
* The designated constructor.
*/
@@ -138,8 +118,7 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
IPluginTaskInfoProvider infoProvider, IFreeSpaceProvider freeSpaceProvider,
IShareIdManager shareIdManager, IHierarchicalContentProvider contentProvider)
{
- this(openBISService, apiServer, infoProvider, null, freeSpaceProvider, shareIdManager,
- contentProvider, new PutDataSetService(openBISService, operationLog));
+ this(openBISService, apiServer, infoProvider, null, freeSpaceProvider, shareIdManager, contentProvider);
}
/**
@@ -148,8 +127,7 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
public DataStoreServerApi(IEncapsulatedOpenBISService openBISService,
IQueryApiServer apiServer, IPluginTaskInfoProvider infoProvider,
IStreamRepository streamRepository, IFreeSpaceProvider freeSpaceProvider,
- IShareIdManager shareIdManager, IHierarchicalContentProvider contentProvider,
- PutDataSetService service)
+ IShareIdManager shareIdManager, IHierarchicalContentProvider contentProvider)
{
super(openBISService, streamRepository, shareIdManager, contentProvider);
// queryApiServer = apiServer;
@@ -345,80 +323,24 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
return new DataStoreServerApiLogger(context);
}
- private NewDataSetDTO getNewDataSet(FullDataSetCreation dataSetCreation, File temporaryIncomingDir) throws IOException
- {
- ISampleId sampleIdentifier = dataSetCreation.getMetadataCreation().getSampleId();
- IExperimentId experimentIdentifier = dataSetCreation.getMetadataCreation().getExperimentId();
- DataSetOwnerType ownerType = DataSetOwnerType.SAMPLE;
- DataSetOwner owner = null;
- if (sampleIdentifier != null)
- {
- owner = new NewDataSetDTO.DataSetOwner(ownerType, sampleIdentifier.toString());
- } else if (experimentIdentifier != null)
- {
- ownerType = DataSetOwnerType.EXPERIMENT;
- owner = new NewDataSetDTO.DataSetOwner(ownerType, experimentIdentifier.toString());
- }
- 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(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());
- }
-
- private List<FullDataSetCreation> filterNonPhysicalDataSets(List<FullDataSetCreation> newDataSets)
+ @Override
+ @Transactional
+ @RolesAllowed({ RoleWithHierarchy.PROJECT_USER })
+ public DataSetPermId createUploadedDataSet(String sessionToken, UploadedDataSetCreation creation)
{
- return newDataSets
- .stream()
- .filter((dataSetCreation) -> dataSetCreation.getMetadataCreation().getPhysicalData() == null)
- .collect(Collectors.toList());
+ return createUploadedDataSetExecutor.create(sessionToken, creation);
}
@Override
@Transactional
@RolesAllowed({ RoleWithHierarchy.INSTANCE_ADMIN })
public List<DataSetPermId> createDataSets(String sessionToken, List<FullDataSetCreation> newDataSets)
- {
- injectDataStoreIdAndCodesIfNeeded(newDataSets);
- List<FullDataSetCreation> physicalDataSets = filterPhysicalDataSets(newDataSets);
- createPhysicalDataSets(sessionToken, physicalDataSets);
-
- List<FullDataSetCreation> nonPhysicalDataSets = filterNonPhysicalDataSets(newDataSets);
- return createNonPhysicalDataSets(sessionToken, nonPhysicalDataSets);
- }
-
- private List<DataSetPermId> createNonPhysicalDataSets(String sessionToken, List<FullDataSetCreation> newDataSets)
{
if (PathInfoDataSourceProvider.isDataSourceDefined() == false)
{
throw new IllegalStateException("Pathinfo DB not configured - cannot store dataset file information");
}
-
+ injectDataStoreIdAndCodesIfNeeded(newDataSets);
IPathsInfoDAO dao = QueryTool.getQuery(PathInfoDataSourceProvider.getDataSource(), IPathsInfoDAO.class);
for (int i = 0; i < newDataSets.size(); i++)
@@ -453,42 +375,6 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
return as.createDataSets(sessionToken, metadata);
}
- private void createPhysicalDataSets(String sessionToken, List<FullDataSetCreation> newDataSets)
- {
- for (FullDataSetCreation dataSetCreation : newDataSets)
- {
- PutDataSetService putService =
- new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
- putService.setStoreDirectory(ServiceProvider.getConfigProvider().getStoreRoot());
- NewDataSetDTO newDataset;
- try
- {
- DataSetCreation metadataCreation = dataSetCreation.getMetadataCreation();
- CreationId creationId = metadataCreation.getCreationId();
- String dataSetTypeCodeNull = null;
- IEntityTypeId typeId = metadataCreation.getTypeId();
- if (null != typeId)
- {
- if (typeId instanceof EntityTypePermId)
- {
- dataSetTypeCodeNull = ((EntityTypePermId) typeId).getPermId();
- } else
- {
- throw new UnsupportedObjectIdException(typeId);
- }
- }
- 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/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiJson.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiJson.java
index f4a3faa402a919bfb65fdbded09f114a93b4459f..7d6e3cc79130e3b9d05c76ea517d770b86cff50c 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiJson.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiJson.java
@@ -27,6 +27,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
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.dataset.create.UploadedDataSetCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
@@ -59,6 +60,12 @@ public class DataStoreServerApiJson implements IDataStoreServerApi
throw new UnsupportedOperationException("This method is not supported in JSON API");
}
+ @Override
+ public DataSetPermId createUploadedDataSet(String sessionToken, UploadedDataSetCreation newDataSet)
+ {
+ return api.createUploadedDataSet(sessionToken, newDataSet);
+ }
+
@Override
public List<DataSetPermId> createDataSets(String sessionToken, List<FullDataSetCreation> newDataSets)
{
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiLogger.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiLogger.java
index dbb7dae12d37d7410c3259d4dd785b591ec8df82..ec7f3ccbe8d6190b4675a49b08eb17700debee4d 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiLogger.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApiLogger.java
@@ -7,6 +7,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
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.dataset.create.UploadedDataSetCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
@@ -50,6 +51,13 @@ public class DataStoreServerApiLogger extends AbstractServerLogger implements
return null;
}
+ @Override
+ public DataSetPermId createUploadedDataSet(String sessionToken, UploadedDataSetCreation newDataSet)
+ {
+ logAccess(sessionToken, "create-uploaded-data-sets", "DATA_SETS:\n%s", newDataSet);
+ return null;
+ }
+
@Override
public List<DataSetPermId> createDataSets(String sessionToken, List<FullDataSetCreation> newDataSets)
{
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/CreateUploadedDataSetExecutor.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/CreateUploadedDataSetExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..ae944447b24b1800d8e6c30226871c88166192f5
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/CreateUploadedDataSetExecutor.java
@@ -0,0 +1,224 @@
+/*
+ * Copyright 2018 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.ethz.sis.openbis.generic.server.dssapi.v3.executor;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.IExperimentId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.ISampleId;
+import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.ObjectNotFoundException;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.UploadedDataSetCreation;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.OperationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.utils.ExceptionUtils;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.etlserver.api.v1.PutDataSetService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class CreateUploadedDataSetExecutor implements ICreateUploadedDataSetExecutor
+{
+
+ private static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION, CreateUploadedDataSetExecutor.class);
+
+ private PutDataSetService putService;
+
+ @Override
+ public DataSetPermId create(String sessionToken, UploadedDataSetCreation creation)
+ {
+ try
+ {
+ getOpenBIService().checkSession(sessionToken);
+
+ NewDataSetDTO newDataset = getNewDataSet(sessionToken, creation);
+
+ List<DataSetInformation> dataSetInfos = getPutService().putDataSet(sessionToken, newDataset, creation.getUploadId());
+
+ if (dataSetInfos != null && false == dataSetInfos.isEmpty())
+ {
+ return new DataSetPermId(dataSetInfos.get(0).getDataSetCode());
+ } else
+ {
+ return null;
+ }
+ } catch (IOException e)
+ {
+ throw ExceptionUtils.create(new OperationContext(null), e);
+ }
+ }
+
+ private NewDataSetDTO getNewDataSet(String sessionToken, UploadedDataSetCreation creation) throws IOException
+ {
+ DataSetOwnerType ownerType;
+ DataSetOwner owner;
+ String typeCode;
+ List<String> parentCodes = new ArrayList<String>();
+
+ // type
+
+ if (creation.getTypeId() != null)
+ {
+ DataSetTypeSearchCriteria criteria = new DataSetTypeSearchCriteria();
+ criteria.withId().thatEquals(creation.getTypeId());
+
+ SearchResult<DataSetType> searchResult =
+ getApplicationServerApi().searchDataSetTypes(sessionToken, criteria, new DataSetTypeFetchOptions());
+
+ if (searchResult.getObjects() != null && false == searchResult.getObjects().isEmpty())
+ {
+ DataSetType type = searchResult.getObjects().get(0);
+ typeCode = type.getCode();
+ } else
+ {
+ throw new ObjectNotFoundException(creation.getTypeId());
+ }
+ } else
+ {
+ throw new UserFailureException("A dataset needs a type.");
+ }
+
+ // owner
+
+ if (creation.getSampleId() != null)
+ {
+ Map<ISampleId, Sample> samples =
+ getApplicationServerApi().getSamples(sessionToken, Arrays.asList(creation.getSampleId()), new SampleFetchOptions());
+ Sample sample = samples.get(creation.getSampleId());
+
+ if (sample == null)
+ {
+ throw new ObjectNotFoundException(creation.getSampleId());
+ }
+
+ ownerType = DataSetOwnerType.SAMPLE;
+ owner = new NewDataSetDTO.DataSetOwner(ownerType, sample.getIdentifier().getIdentifier());
+ } else if (creation.getExperimentId() != null)
+ {
+ Map<IExperimentId, Experiment> experiments =
+ getApplicationServerApi().getExperiments(sessionToken, Arrays.asList(creation.getExperimentId()), new ExperimentFetchOptions());
+ Experiment experiment = experiments.get(creation.getExperimentId());
+
+ if (experiment == null)
+ {
+ throw new ObjectNotFoundException(creation.getExperimentId());
+ }
+
+ ownerType = DataSetOwnerType.EXPERIMENT;
+ owner = new NewDataSetDTO.DataSetOwner(ownerType, experiment.getIdentifier().getIdentifier());
+ } else
+ {
+ throw new UserFailureException("A dataset needs either a sample or an experiment as an owner.");
+ }
+
+ // parents
+
+ if (creation.getParentIds() != null && false == creation.getParentIds().isEmpty())
+ {
+ Map<IDataSetId, DataSet> parents =
+ getApplicationServerApi().getDataSets(sessionToken, creation.getParentIds(), new DataSetFetchOptions());
+
+ for (IDataSetId parentId : creation.getParentIds())
+ {
+ DataSet parent = parents.get(parentId);
+ if (parent == null)
+ {
+ throw new ObjectNotFoundException(parentId);
+ }
+ parentCodes.add(parent.getCode());
+ }
+ }
+
+ // upload id
+
+ if (creation.getUploadId() != null)
+ {
+ if (creation.getUploadId().contains("/"))
+ {
+ throw new UserFailureException("Upload id must not contain '/'");
+ }
+
+ File temporaryIncomingRoot = getPutService().getTemporaryIncomingRoot(typeCode);
+ File temporaryIncomingDir = new File(temporaryIncomingRoot, creation.getUploadId());
+
+ if (false == temporaryIncomingDir.exists())
+ {
+ throw new UserFailureException(
+ "The folder for the upload id " + creation.getUploadId() + " could not be found. Have you uploaded the file(s) first?");
+ }
+ } else
+ {
+ throw new UserFailureException("Upload id cannot be null.");
+ }
+
+ NewDataSetDTO newDataSet = new NewDataSetDTO(typeCode, owner, null, new ArrayList<FileInfoDssDTO>());
+ newDataSet.setProperties(creation.getProperties());
+ newDataSet.setParentDataSetCodes(parentCodes);
+ return newDataSet;
+ }
+
+ private IApplicationServerApi getApplicationServerApi()
+ {
+ return ServiceProvider.getV3ApplicationService();
+ }
+
+ private IEncapsulatedOpenBISService getOpenBIService()
+ {
+ return ServiceProvider.getOpenBISService();
+ }
+
+ private synchronized PutDataSetService getPutService()
+ {
+ if (putService == null)
+ {
+ putService = new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
+ putService.setStoreDirectory(ServiceProvider.getConfigProvider().getStoreRoot());
+ }
+
+ return putService;
+ }
+}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/ICreateUploadedDataSetExecutor.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/ICreateUploadedDataSetExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..995215e6cbab5a122902a9e69346389d2e41a665
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/executor/ICreateUploadedDataSetExecutor.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2018 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.ethz.sis.openbis.generic.server.dssapi.v3.executor;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.UploadedDataSetCreation;
+
+/**
+ * @author pkupczyk
+ */
+public interface ICreateUploadedDataSetExecutor
+{
+
+ DataSetPermId create(String sessionToken, UploadedDataSetCreation creation);
+
+}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/upload/StoreShareFileUploadServlet.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/upload/StoreShareFileUploadServlet.java
index 4730bf93a4b5710504a3c1aa2e0ab79c0898f811..e40df8eeb44a5fb311da1d059dedbd6e299243bb 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/upload/StoreShareFileUploadServlet.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/upload/StoreShareFileUploadServlet.java
@@ -29,20 +29,14 @@ import org.apache.commons.fileupload.FileItemIterator;
import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.servlet.ServletFileUpload;
+import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
-import org.springframework.stereotype.Component;
-import org.springframework.stereotype.Controller;
import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.bind.annotation.RestController;
-import com.marathon.util.spring.StreamSupportingHttpInvokerServiceExporter;
-
-import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
-import ch.ethz.sis.openbis.generic.server.dssapi.v3.DataStoreServerApiJsonServer;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.etlserver.api.v1.PutDataSetService;
@@ -50,21 +44,23 @@ import ch.systemsx.cisd.openbis.dss.generic.server.Utils;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
/**
- *
- *
* @author Ganime Betul Akin
*/
@RestController
-@RequestMapping({"store_share_file_upload", "/datastore_server/store_share_file_upload"})
+@RequestMapping({ "store_share_file_upload", "/datastore_server/store_share_file_upload" })
public class StoreShareFileUploadServlet extends HttpServlet
{
private static final long serialVersionUID = 1L;
-
- @SuppressWarnings("hiding")
+
protected static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
StoreShareFileUploadServlet.class);
+ public static final String SESSION_ID_PARAM = Utils.SESSION_ID_PARAM;
+
public static final String DATA_SET_TYPE_PARAM = "dataSetType";
+
+ public static final String IGNORE_FILE_PATH_PARAM = "ignoreFilePath";
+
public static final String UPLOAD_ID_PARAM = "uploadID";
private PutDataSetService putService;
@@ -73,27 +69,27 @@ public class StoreShareFileUploadServlet extends HttpServlet
public final void init(final ServletConfig servletConfig) throws ServletException
{
super.init(servletConfig);
- this.putService =
- new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
+ this.putService = new PutDataSetService(ServiceProvider.getOpenBISService(), operationLog);
putService.setStoreDirectory(ServiceProvider.getConfigProvider().getStoreRoot());
-
}
+
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException
{
- StoreShareFileUploadRequest uploadRequest =
- new StoreShareFileUploadRequest(request);
+ StoreShareFileUploadRequest uploadRequest = new StoreShareFileUploadRequest(request);
uploadRequest.validate();
-
- String dataSetTypeCodeOrNull = uploadRequest.getDataSetType();
- String uploadId = uploadRequest.getUploadId();
try
{
FileItemIterator iterator = uploadRequest.getFiles();
+ if (false == iterator.hasNext())
+ {
+ throw new UserFailureException("Please upload at least one file");
+ }
+
while (iterator.hasNext())
{
FileItemStream file = null;
@@ -103,23 +99,30 @@ public class StoreShareFileUploadServlet extends HttpServlet
{
file = iterator.next();
stream = file.openStream();
- putService.putFileToStoreShare(uploadRequest.getSessionId(), file.getName(), dataSetTypeCodeOrNull, uploadId, stream);
- }
- catch (Exception e) {
- operationLog.error(e.getMessage());
- }
- finally
+
+ /*
+ * Most browsers send only base file names for files which were uploaded via a regular html form. Still, there are some browsers
+ * (e.g. Opera) that are known to send file paths as well. To handle all browsers consistently by default we ignore file paths
+ * even if they are given. We only use the file paths if it has been explicitly requested via <code>IGNORE_FILE_PATH_PARAM</code>
+ * request parameter. This may be handy in contexts where we have a full control over what gets sent to the servlet (e.g. from a
+ * Python script that makes http requests to the servlet).
+ */
+ String filePath = uploadRequest.isIgnoreFilePath() ? FilenameUtils.getName(file.getName()) : file.getName();
+
+ putService.putFileToStoreShare(uploadRequest.getSessionId(), filePath, uploadRequest.getDataSetType(),
+ uploadRequest.getUploadId(), stream);
+ } finally
{
IOUtils.closeQuietly(stream);
}
}
-
- } catch (FileUploadException e)
+ } catch (Exception e)
{
+ operationLog.error(e.getMessage());
throw CheckedExceptionTunnel.wrapIfNecessary(e);
}
}
-
+
private class StoreShareFileUploadRequest
{
@@ -132,8 +135,9 @@ public class StoreShareFileUploadServlet extends HttpServlet
public String getSessionId()
{
- return request.getParameter(Utils.SESSION_ID_PARAM);
+ return request.getParameter(SESSION_ID_PARAM);
}
+
public String getDataSetType()
{
return request.getParameter(DATA_SET_TYPE_PARAM);
@@ -144,6 +148,19 @@ public class StoreShareFileUploadServlet extends HttpServlet
return request.getParameter(UPLOAD_ID_PARAM);
}
+ public boolean isIgnoreFilePath()
+ {
+ String str = request.getParameter(IGNORE_FILE_PATH_PARAM);
+
+ if (str == null || str.isEmpty())
+ {
+ return true;
+ } else
+ {
+ return Boolean.valueOf(str);
+ }
+ }
+
public FileItemIterator getFiles() throws FileUploadException, IOException
{
ServletFileUpload upload = new ServletFileUpload();
@@ -154,18 +171,7 @@ public class StoreShareFileUploadServlet extends HttpServlet
{
if (ServletFileUpload.isMultipartContent(request) == false)
{
- throw new IllegalArgumentException(
- "The session workspace form upload accepts only multipart requests");
- }
- if (getSessionId() == null)
- {
- throw new IllegalArgumentException(Utils.SESSION_ID_PARAM
- + " parameter cannot be null");
- }
-
- if (getUploadId() == null)
- {
- throw new IllegalArgumentException(UPLOAD_ID_PARAM + " parameter cannot be null");
+ throw new UserFailureException("The file upload accepts only multipart requests");
}
}
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 8ca00943510e01c3d2801b1bb9fa3fec08161551..0b2fd226dd604209bc4a3269523e886ccdcc8977 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
@@ -135,7 +135,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
}
PutDataSetExecutor(PutDataSetService service, IETLServerPlugin plugin, String sessionToken,
- NewDataSetDTO newDataSet, File temporaryIncomingDir)
+ NewDataSetDTO newDataSet, File temporaryIncomingDir, File dataSet)
{
this.service = service;
this.plugin = plugin;
@@ -144,17 +144,7 @@ class PutDataSetExecutor implements IDataSetHandlerRpc
this.inputStream = null;
this.copier = FastRecursiveHardLinkMaker.tryCreate(RSyncConfig.getInstance().getAdditionalCommandLineOptions());
this.temporaryIncomingDir = temporaryIncomingDir;
- this.dataSetDir = new File(temporaryIncomingDir, newDataSet.getDataSetFolderName());
- if (dataSetDir.exists())
- {
- deleteDataSetDir();
- }
- if (false == this.dataSetDir.mkdir())
- {
- throw new EnvironmentFailureException("Could not create directory for data set "
- + newDataSet.getDataSetFolderName());
- }
-
+ this.dataSetDir = dataSet;
overridingTypeExtractor = new OverridingTypeExtractor();
handler = plugin.getDataSetHandler(this, service.getOpenBisService());
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
index c5e75e0e6f6faa4670e4ed8c85c0d3236573f544..f1e8fe136846c1aa27fd28d3c9e10ec557ccb478 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
@@ -65,6 +65,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
*/
public class PutDataSetService
{
+
+ private static final String MULTIPLE_FILES_UPLOAD_DIR = "upload";
+
private final IEncapsulatedOpenBISService openBisService;
private final Logger operationLog;
@@ -258,8 +261,8 @@ public class PutDataSetService
}
}
}
-
- public String putDataSet(String sessionToken, NewDataSetDTO newDataSet, String uploadId, String dataSetCode)
+
+ public List<DataSetInformation> putDataSet(String sessionToken, NewDataSetDTO newDataSet, String uploadId)
throws IOExceptionUnchecked, IllegalArgumentException
{
if (false == isInitialized)
@@ -267,101 +270,111 @@ public class PutDataSetService
doInitialization();
}
- try
+ String dataSetTypeOrNull = newDataSet.tryDataSetType();
+ ITopLevelDataSetRegistrator registrator = registratorMap.getRegistratorForType(dataSetTypeOrNull);
+
+ File uploadDir = new File(getTemporaryIncomingRoot(dataSetTypeOrNull), uploadId);
+ File multipleFilesUploadDir = new File(uploadDir, MULTIPLE_FILES_UPLOAD_DIR);
+ File[] uploadedFiles = multipleFilesUploadDir.listFiles();
+ File dataSet = null;
+
+ if (uploadedFiles != null && uploadedFiles.length == 1)
{
- String dataSetTypeOrNull = newDataSet.tryDataSetType();
- ITopLevelDataSetRegistrator registrator =
- registratorMap.getRegistratorForType(dataSetTypeOrNull);
+ dataSet = uploadedFiles[0];
+ } else
+ {
+ dataSet = multipleFilesUploadDir;
+ }
- File uploadedDataSetDir =
- new File(getTemporaryIncomingRoot(dataSetTypeOrNull), uploadId);
+ if (registrator instanceof PutDataSetServerPluginHolder)
+ {
+ return new PutDataSetExecutor(this, ((PutDataSetServerPluginHolder) registrator).getPlugin(), sessionToken, newDataSet, uploadDir,
+ dataSet).executeWithoutWriting();
+ } else
+ {
+ return new PutDataSetTopLevelDataSetHandler(this, registrator, sessionToken, newDataSet, uploadDir, dataSet).executeWithoutWriting();
+ }
+ }
- File temporaryDataSetDir =
- new File(getTemporaryIncomingRoot(dataSetTypeOrNull), dataSetCode);
-
- if(false == uploadedDataSetDir.renameTo(temporaryDataSetDir)) {
- throw new ConfigurationFailureException("Could not rename : "
- + uploadedDataSetDir + " to " + temporaryDataSetDir);
+ public void putFileToStoreShare(String sessionToken, String filePath, String dataSetType, String uploadId, InputStream inputStream)
+ {
+ if (false == isInitialized)
+ {
+ doInitialization();
+ }
- }
+ File file = null;
+ OutputStream outputStream = null;
- final List<DataSetInformation> infos;
- // Branch -- use the old logic for the ETLServerPlugins
- if (registrator instanceof PutDataSetServerPluginHolder)
+ try
+ {
+ if (StringUtils.isBlank(sessionToken))
{
- infos =
- new PutDataSetExecutor(this,
- ((PutDataSetServerPluginHolder) registrator).getPlugin(),
- sessionToken, newDataSet, temporaryDataSetDir).executeWithoutWriting();
- } else
+ throw new UserFailureException("Session token cannot be null or empty");
+ }
+ if (StringUtils.isBlank(filePath))
{
- infos =
- new PutDataSetTopLevelDataSetHandler(this, registrator, sessionToken,
- newDataSet, temporaryDataSetDir).executeWithoutWriting();
+ throw new UserFailureException("File path cannot be null or empty");
}
- StringBuilder sb = new StringBuilder();
- for (DataSetInformation info : infos)
+ if (filePath.contains("../"))
{
- sb.append(info.getDataSetCode());
- sb.append(",");
+ throw new UserFailureException("File path must not contain '../'");
+ }
+ if (StringUtils.isBlank(dataSetType))
+ {
+ throw new UserFailureException("Data set type cannot be null or empty");
+ }
+ if (StringUtils.isBlank(uploadId))
+ {
+ throw new UserFailureException("Upload id cannot be null or empty");
+ }
+ if (uploadId.contains("/"))
+ {
+ throw new UserFailureException("Upload id must not contain '/'");
+ }
+ if (inputStream == null)
+ {
+ throw new UserFailureException("Input stream cannot be null");
}
- // Remove the trailing comma
- if (sb.length() > 0)
+ ServiceProvider.getOpenBISService().checkSession(sessionToken);
+
+ File uploadDir = new File(getTemporaryIncomingRoot(dataSetType), uploadId);
+ if (false == uploadDir.exists())
{
- sb.deleteCharAt(sb.length() - 1);
+ uploadDir.mkdir();
}
- return sb.toString();
- } catch (UserFailureException e)
- {
- throw new IllegalArgumentException(e);
- }
- }
- public String putFileToStoreShare(String sessionToken, String filePath, String dataSetTypeCodeOrNull, String uploadId, InputStream inputStream) {
- {
- if (false == isInitialized)
+
+ File uploadSubDir = new File(uploadDir, MULTIPLE_FILES_UPLOAD_DIR);
+ if (false == uploadSubDir.exists())
{
- doInitialization();
+ uploadSubDir.mkdir();
}
+ File filePathDir = new File(uploadSubDir, FilenameUtils.getPath(filePath));
+ filePathDir.mkdirs();
+
+ file = new File(filePathDir, FilenameUtils.getName(filePath));
+ outputStream = new FileOutputStream(file);
+
+ IOUtils.copyLarge(inputStream, outputStream);
+
+ } catch (IOException ioe)
+ {
+ IOUtils.closeQuietly(outputStream);
+
try
{
- ServiceProvider.getOpenBISService().checkSession(sessionToken);
- if (filePath.contains("../"))
- {
- throw new IOExceptionUnchecked("filePath must not contain '../'");
- }
- String uniqueFolderName = uploadId;
- File temporaryDataSetDir =
- new File(getTemporaryIncomingRoot(dataSetTypeCodeOrNull), uniqueFolderName);
- if(false == temporaryDataSetDir.exists()) {
- temporaryDataSetDir.mkdir();
- }
- final String subDir = FilenameUtils.getFullPath(filePath);
- final String filename = FilenameUtils.getName(filePath);
- final File dir = new File(temporaryDataSetDir, subDir);
- dir.mkdirs();
- final File file = new File(dir, filename);
- OutputStream ostream = null;
- try
- {
- ostream = new FileOutputStream(file);
- long size = IOUtils.copyLarge(inputStream, ostream);
- ostream.close();
- return uniqueFolderName;
- } catch (IOException ex)
- {
- file.delete();
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- } finally
- {
- IOUtils.closeQuietly(ostream);
- }
- }
- catch (UserFailureException e)
+ file.delete();
+ } catch (Exception e)
{
- throw new IllegalArgumentException(e);
- }
+ }
+
+ throw CheckedExceptionTunnel.wrapIfNecessary(ioe);
+
+ } finally
+ {
+ IOUtils.closeQuietly(outputStream);
}
}
@@ -491,28 +504,7 @@ public class PutDataSetService
return temporaryIncomingDir;
}
- private File getTemporaryIncomingRoot(String dataSetTypeCodeOrNull)
- {
- TopLevelDataSetRegistratorGlobalState globalState =
- getThreadGlobalState(dataSetTypeCodeOrNull);
- File storeRoot = globalState.getStoreRootDir();
- if (false == StringUtils.isBlank(globalState.getShareId()))
- {
- File shareRoot = new File(storeRoot, globalState.getShareId());
- if (shareRoot.isDirectory())
- {
- File incomingDir = new File(shareRoot, "rpc-incoming");
- incomingDir.mkdir();
- if (incomingDir.isDirectory())
- {
- return incomingDir;
- }
- }
- }
- return storeRoot;
- }
-
- public File getTemporaryIncomingDir(String dataSetTypeCodeOrNull, String creationId)
+ public File getTemporaryIncomingRoot(String dataSetTypeCodeOrNull)
{
if (false == isInitialized)
{
@@ -528,15 +520,18 @@ public class PutDataSetService
if (shareRoot.isDirectory())
{
File incomingDir = new File(shareRoot, "rpc-incoming");
- File tempDir = new File(incomingDir, creationId);
- if(false == tempDir.exists()) {
- throw new UserFailureException("The folder for the creation Id " + creationId + " could not be found. Have you uploaded the file first?" );
+ incomingDir.mkdir();
+ if (incomingDir.isDirectory())
+ {
+ return incomingDir;
}
}
}
return storeRoot;
}
+
}
+
/**
* Helper class to simplify initializing the final fields of the {@link PutDataSetService}.
*
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 abc85f9fb6e4117f3b628b2b39a1652661c390ef..8722cbba53ddb2d616154f5e6ca8609e369b609d 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
@@ -98,39 +98,16 @@ class PutDataSetTopLevelDataSetHandler
private final File dataSet;
PutDataSetTopLevelDataSetHandler(PutDataSetService service,
- ITopLevelDataSetRegistrator registrator, String sessionToken, NewDataSetDTO newDataSet, File temporaryIncomingDir)
+ ITopLevelDataSetRegistrator registrator, String sessionToken, NewDataSetDTO newDataSet, File temporaryIncomingDir, File dataSet)
{
this.service = service;
this.registrator = registrator;
this.sessionToken = sessionToken;
this.newDataSet = newDataSet;
this.temporaryIncomingDir = temporaryIncomingDir;
+ this.dataSet = dataSet;
this.inputStream = null;
- String dataSetFolderName = newDataSet.getDataSetFolderName();
- boolean dataSetIsASingleFile =
- NewDataSetDTO.DEFAULT_DATA_SET_FOLDER_NAME.equals(dataSetFolderName)
- && newDataSet.getFileInfos().size() == 1;
- if (dataSetIsASingleFile)
- {
- dataSetDir = temporaryIncomingDir;
- dataSet =
- new File(temporaryIncomingDir, newDataSet.getFileInfos().get(0)
- .getPathInDataSet());
- } else
- {
- this.dataSetDir = new File(temporaryIncomingDir, dataSetFolderName);
- dataSet = dataSetDir;
- }
- if (dataSetDir.exists())
- {
- deleteDataSetDir();
- }
- if (false == this.dataSetDir.mkdir())
- {
- throw new EnvironmentFailureException("Could not create directory for data set "
- + dataSet.getName());
- }
-
+ this.dataSetDir = null;
}
PutDataSetTopLevelDataSetHandler(PutDataSetService service,
diff --git a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/CreateUploadedDataSetsTest.java b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/CreateUploadedDataSetsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..53f8ef2a2d9bc8f5479cfb95e161680c7994f55b
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/CreateUploadedDataSetsTest.java
@@ -0,0 +1,916 @@
+/*
+ * Copyright 2017 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.dss.systemtest.api.v3;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeoutException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.exception.ExceptionUtils;
+import org.eclipse.jetty.client.HttpClient;
+import org.eclipse.jetty.client.api.ContentResponse;
+import org.eclipse.jetty.client.api.Request;
+import org.eclipse.jetty.client.util.MultiPartContentProvider;
+import org.eclipse.jetty.client.util.StringContentProvider;
+import org.eclipse.jetty.http.HttpMethod;
+import org.eclipse.jetty.http.HttpStatus;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.UploadedDataSetCreation;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.DataSetFilePermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.IDataSetFileId;
+import ch.ethz.sis.openbis.generic.server.dssapi.v3.upload.StoreShareFileUploadServlet;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.util.TestInstanceHostUtils;
+import ch.systemsx.cisd.openbis.systemtest.authorization.ProjectAuthorizationUser;
+
+/**
+ * @author Ganime Betul Akin
+ */
+public class CreateUploadedDataSetsTest extends AbstractFileTest
+{
+ private static final String SERVICE_URL = TestInstanceHostUtils.getDSSUrl() + "/datastore_server/store_share_file_upload";
+
+ private IApplicationServerApi as;
+
+ @Override
+ @BeforeClass
+ protected void beforeClass() throws Exception
+ {
+ super.beforeClass();
+ as = ServiceProvider.getV3ApplicationService();
+ }
+
+ @Test
+ public void testUploadWithInvalidSession() throws Exception
+ {
+ ContentResponse response =
+ uploadFiles("admin-180211214633760xF769DD44CAFFAF7B50FBEADF00DBEE1F", UUID.randomUUID().toString(), "UNKNOWN", true,
+ new FileToUpload());
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("user is not logged in"));
+ }
+
+ @Test
+ public void testUploadWithoutSession() throws Exception
+ {
+ ContentResponse response = uploadFiles(null, UUID.randomUUID().toString(), "UNKNOWN", true, new FileToUpload());
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("Session token cannot be null or empty"));
+ }
+
+ @Test
+ public void testUploadWithoutType() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response = uploadFiles(sessionToken, UUID.randomUUID().toString(), null, true, new FileToUpload());
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("Data set type cannot be null or empty"));
+ }
+
+ @Test
+ public void testUploadWithoutUploadId() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response = uploadFiles(sessionToken, null, "UNKNOWN", true, new FileToUpload());
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("Upload id cannot be null or empty"));
+ }
+
+ @Test
+ public void testUploadWithUploadIdThatContainsSlash() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response = uploadFiles(sessionToken, "iam/incorrect", "UNKNOWN", true, new FileToUpload());
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("Upload id must not contain '/'"));
+ }
+
+ @Test
+ public void testUploadWithoutFile() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response = uploadFiles(sessionToken, UUID.randomUUID().toString(), "UNKNOWN", true);
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("Please upload at least one file"));
+ }
+
+ @Test
+ public void testUploadWithFileWithFolderUpPath() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response =
+ uploadFiles(sessionToken, UUID.randomUUID().toString(), "UNKNOWN", false, new FileToUpload("name", "iam/../incorrect", "content"));
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("File path must not contain '../'"));
+ }
+
+ @Test
+ public void testUploadWithFileWithoutPath() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ ContentResponse response =
+ uploadFiles(sessionToken, UUID.randomUUID().toString(), "UNKNOWN", false, new FileToUpload("name", null, "content"));
+ assertResponseError(response);
+ assertTrue(response.getContentAsString(), response.getContentAsString().contains("File path cannot be null or empty"));
+ }
+
+ @Test
+ public void testCreateWithInvalidSession() throws Exception
+ {
+ try
+ {
+ getCreateAndGetDataSet("admin-180211214633760xF769DD44CAFFAF7B50FBEADF00DBEE1F", null);
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("user is not logged in"));
+ }
+ }
+
+ @Test
+ public void testCreateWithoutType() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String sampleIdentifier = "/CISD/CP-TEST-1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setSampleId(new SampleIdentifier(sampleIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("A dataset needs a type"));
+ }
+ }
+
+ @Test
+ public void testCreateWithTypeNonexistent() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "IDONTEXIST";
+ String sampleIdentifier = "/CISD/CP-TEST-1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setSampleId(new SampleIdentifier(sampleIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("Object with EntityTypePermId = [IDONTEXIST, null] has not been found"));
+ }
+ }
+
+ @Test
+ public void testCreateWithoutOwner() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("A dataset needs either a sample or an experiment as an owner"));
+ }
+ }
+
+ @Test
+ public void testCreateWithSampleNonexistent() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String sampleIdentifier = "/IDONTEXIST/IDONTEXIST";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setSampleId(new SampleIdentifier(sampleIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("Object with SampleIdentifier = [/IDONTEXIST/IDONTEXIST] has not been found"));
+ }
+ }
+
+ @Test
+ public void testCreateWithSampleIdentifier() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String sampleIdentifier = "/CISD/CP-TEST-1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setSampleId(new SampleIdentifier(sampleIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(sampleIdentifier, dataSet.getSample().getIdentifier().getIdentifier());
+ }
+
+ @Test
+ public void testCreateWithSamplePermId() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String samplePermId = "200902091219327-1025";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setSampleId(new SamplePermId(samplePermId));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(samplePermId, dataSet.getSample().getPermId().getPermId());
+ }
+
+ @Test
+ public void testCreateWithExperimentNonexistent() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/IDONTEXIST/IDONTEXIST/IDONTEXIST";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(),
+ e.getMessage().contains("Object with ExperimentIdentifier = [/IDONTEXIST/IDONTEXIST/IDONTEXIST] has not been found"));
+ }
+ }
+
+ @Test
+ public void testCreateWithExperimentIdentifier() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+ }
+
+ @Test
+ public void testCreateWithExperimentPermId() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentPermId = "200811050951882-1028";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentPermId(experimentPermId));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentPermId, dataSet.getExperiment().getPermId().getPermId());
+ }
+
+ @Test
+ public void testCreateWithProperties() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "HCS_IMAGE";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ Map<String, String> properties = new HashMap<String, String>();
+ properties.put("COMMENT", "test comment");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+ creation.setProperties(properties);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+ assertEquals("test comment", dataSet.getProperty("COMMENT"));
+ }
+
+ @Test
+ public void testCreateWithParentIds() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+ IDataSetId parentId = new DataSetPermId("20081105092159111-1");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setParentIds(Arrays.asList(parentId));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, new FileToUpload());
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+ assertEquals(1, dataSet.getParents().size());
+ assertEquals(parentId, dataSet.getParents().get(0).getPermId());
+ }
+
+ @Test
+ public void testCreateWithoutUploadId() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("Upload id cannot be null"));
+ }
+ }
+
+ @Test
+ public void testCreateWithUploadIdThatContainsSlash() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId("iam/incorrect");
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains("Upload id must not contain '/'"));
+ }
+ }
+
+ @Test
+ public void testCreateWithoutUpload() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail();
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(),
+ e.getMessage()
+ .contains("The folder for the upload id " + uploadId + " could not be found. Have you uploaded the file(s) first?"));
+ }
+ }
+
+ @Test
+ public void testCreateWithSingleFile() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ FileToUpload file = new FileToUpload("file", "test.txt", "test content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, false, file);
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+
+ List<DownloadedFile> files = downloadFiles(sessionToken, dataSet.getPermId());
+ assertEquals(3, files.size());
+
+ assertDirectory(files.get(0), "");
+ assertDirectory(files.get(1), "original");
+ assertFile(files.get(2), "original/test.txt", file.content);
+ }
+
+ @Test
+ public void testCreateWithMultipleFiles() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ FileToUpload file1 = new FileToUpload("file1", "test1.txt", "test1 content");
+ FileToUpload file2 = new FileToUpload("file2", "test2.txt", "test2 content");
+ FileToUpload file3 = new FileToUpload("file3", "folder/test3.txt", "test3 content");
+ FileToUpload file4 = new FileToUpload("file4", "folder/test4.txt", "test4 content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, false, file1, file2, file3, file4);
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+
+ List<DownloadedFile> files = downloadFiles(sessionToken, dataSet.getPermId());
+ assertEquals(8, files.size());
+
+ assertDirectory(files.get(0), "");
+ assertDirectory(files.get(1), "original");
+ assertDirectory(files.get(2), "original/upload");
+ assertDirectory(files.get(3), "original/upload/folder");
+ assertFile(files.get(4), "original/upload/folder/test3.txt", file3.content);
+ assertFile(files.get(5), "original/upload/folder/test4.txt", file4.content);
+ assertFile(files.get(6), "original/upload/test1.txt", file1.content);
+ assertFile(files.get(7), "original/upload/test2.txt", file2.content);
+ }
+
+ @Test
+ public void testCreateWithIgnoreFilePathDefault() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ FileToUpload file1 = new FileToUpload("file1", "test1.txt", "test1 content");
+ FileToUpload file2 = new FileToUpload("file2", "folder/test2.txt", "test2 content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, null, file1, file2);
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+
+ List<DownloadedFile> files = downloadFiles(sessionToken, dataSet.getPermId());
+ assertEquals(5, files.size());
+
+ assertDirectory(files.get(0), "");
+ assertDirectory(files.get(1), "original");
+ assertDirectory(files.get(2), "original/upload");
+ assertFile(files.get(3), "original/upload/test1.txt", file1.content);
+ assertFile(files.get(4), "original/upload/test2.txt", file2.content);
+ }
+
+ @Test
+ public void testCreateWithIgnoreFilePathSetToFalse() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ FileToUpload file1 = new FileToUpload("file1", "test1.txt", "test1 content");
+ FileToUpload file2 = new FileToUpload("file2", "folder/test2.txt", "test2 content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, false, file1, file2);
+ assertResponseOK(response);
+
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+
+ List<DownloadedFile> files = downloadFiles(sessionToken, dataSet.getPermId());
+ assertEquals(6, files.size());
+
+ assertDirectory(files.get(0), "");
+ assertDirectory(files.get(1), "original");
+ assertDirectory(files.get(2), "original/upload");
+ assertDirectory(files.get(3), "original/upload/folder");
+ assertFile(files.get(4), "original/upload/folder/test2.txt", file2.content);
+ assertFile(files.get(5), "original/upload/test1.txt", file1.content);
+ }
+
+ @Test
+ public void testCreateWithMultipleAttempts() throws Exception
+ {
+ String sessionToken = as.login(TEST_USER, PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/CISD/NEMO/EXP1";
+
+ Map<String, String> properties = new HashMap<String, String>();
+ properties.put("IDONTEXIST", "test value");
+
+ FileToUpload file = new FileToUpload("file", "test.txt", "test content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setProperties(properties);
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, file);
+ assertResponseOK(response);
+
+ // first attempt
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail("Creation should have failed because of nonexistent 'IDONTEXIST' property");
+ } catch (Exception e)
+ {
+ String fullStackTrace = ExceptionUtils.getFullStackTrace(e);
+ assertTrue(fullStackTrace, fullStackTrace.contains("Property type with code 'IDONTEXIST' does not exist!"));
+ }
+
+ // second attempt
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ fail("Creation should have failed as uploaded file should have been removed during the first attempt");
+ } catch (Exception e)
+ {
+ String fullStackTrace = ExceptionUtils.getFullStackTrace(e);
+ assertTrue(fullStackTrace, fullStackTrace.contains("The folder for the upload id " + uploadId + " could not be found"));
+ }
+ }
+
+ @Test(dataProviderClass = ProjectAuthorizationUser.class, dataProvider = ProjectAuthorizationUser.PROVIDER)
+ public void testCreateWithProjectAuthorization(ProjectAuthorizationUser user) throws Exception
+ {
+ String sessionToken = as.login(user.getUserId(), PASSWORD);
+
+ String uploadId = UUID.randomUUID().toString();
+ String dataSetType = "UNKNOWN";
+ String experimentIdentifier = "/TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST";
+
+ FileToUpload file = new FileToUpload("file", "test.txt", "test content");
+
+ UploadedDataSetCreation creation = new UploadedDataSetCreation();
+ creation.setTypeId(new EntityTypePermId(dataSetType));
+ creation.setExperimentId(new ExperimentIdentifier(experimentIdentifier));
+ creation.setUploadId(uploadId);
+
+ ContentResponse response = uploadFiles(sessionToken, uploadId, dataSetType, true, file);
+ assertResponseOK(response);
+
+ if (user.isDisabledProjectUser())
+ {
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(), e.getMessage().contains(
+ "None of method roles '[PROJECT_OBSERVER, PROJECT_USER, PROJECT_POWER_USER, PROJECT_ADMIN, SPACE_ADMIN, INSTANCE_ADMIN, SPACE_POWER_USER, SPACE_USER, SPACE_OBSERVER, INSTANCE_OBSERVER, SPACE_ETL_SERVER, INSTANCE_ETL_SERVER]' could be found in roles of user"));
+ }
+ } else if (user.isInstanceUserOrTestSpaceUserOrEnabledTestProjectUser())
+ {
+ DataSet dataSet = getCreateAndGetDataSet(sessionToken, creation);
+
+ assertEquals(dataSetType, dataSet.getType().getCode());
+ assertEquals(experimentIdentifier, dataSet.getExperiment().getIdentifier().getIdentifier());
+
+ List<DownloadedFile> files = downloadFiles(sessionToken, dataSet.getPermId());
+ assertEquals(3, files.size());
+
+ assertDirectory(files.get(0), "");
+ assertDirectory(files.get(1), "original");
+ assertFile(files.get(2), "original/test.txt", file.content);
+ } else
+ {
+ try
+ {
+ getCreateAndGetDataSet(sessionToken, creation);
+ } catch (UserFailureException e)
+ {
+ assertTrue(e.getMessage(),
+ e.getMessage().contains("Object with ExperimentIdentifier = [/TEST-SPACE/TEST-PROJECT/EXP-SPACE-TEST] has not been found"));
+ }
+ }
+ }
+
+ private ContentResponse uploadFiles(String sessionToken, String uploadId, String dataSetType, Boolean ignoreFilePath,
+ FileToUpload... filesToUpload)
+ throws InterruptedException, TimeoutException, ExecutionException
+ {
+ HttpClient client = JettyHttpClientFactory.getHttpClient();
+ MultiPartContentProvider multiPart = new MultiPartContentProvider();
+
+ for (FileToUpload fileToUpload : filesToUpload)
+ {
+ multiPart.addFilePart(fileToUpload.fieldName, fileToUpload.fileName, new StringContentProvider(fileToUpload.content), null);
+ }
+
+ multiPart.close();
+
+ Request request = client.newRequest(SERVICE_URL).method(HttpMethod.POST);
+
+ if (sessionToken != null)
+ {
+ request.param(StoreShareFileUploadServlet.SESSION_ID_PARAM, sessionToken);
+ }
+ if (uploadId != null)
+ {
+ request.param(StoreShareFileUploadServlet.UPLOAD_ID_PARAM, uploadId);
+ }
+ if (ignoreFilePath != null)
+ {
+ request.param(StoreShareFileUploadServlet.IGNORE_FILE_PATH_PARAM, String.valueOf(ignoreFilePath));
+ }
+ if (dataSetType != null)
+ {
+ request.param(StoreShareFileUploadServlet.DATA_SET_TYPE_PARAM, dataSetType);
+ }
+ request.content(multiPart);
+ return request.send();
+ }
+
+ private DataSet getCreateAndGetDataSet(String sessionToken, UploadedDataSetCreation creation)
+ {
+ DataSetPermId permId = dss.createUploadedDataSet(sessionToken, creation);
+ assertNotNull(permId);
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withType();
+ fo.withExperiment();
+ fo.withSample();
+ fo.withProperties();
+ fo.withParents();
+
+ Map<IDataSetId, DataSet> dataSets = as.getDataSets(sessionToken, Arrays.asList(permId), fo);
+ DataSet dataSet = dataSets.get(permId);
+ assertNotNull(dataSet);
+
+ return dataSet;
+ }
+
+ private List<DownloadedFile> downloadFiles(String sessionToken, IDataSetId dataSetId) throws IOException
+ {
+ DataSetFileDownloadOptions options = new DataSetFileDownloadOptions();
+ options.setRecursive(true);
+
+ IDataSetFileId fileId = new DataSetFilePermId(dataSetId, "");
+
+ InputStream stream = dss.downloadFiles(sessionToken, Arrays.asList(fileId), options);
+ DataSetFileDownloadReader reader = new DataSetFileDownloadReader(stream);
+
+ List<DownloadedFile> files = new ArrayList<DownloadedFile>();
+ DataSetFileDownload download = null;
+
+ while ((download = reader.read()) != null)
+ {
+ DownloadedFile file = new DownloadedFile(download.getDataSetFile(), IOUtils.toString(download.getInputStream()));
+ files.add(file);
+ }
+
+ return files;
+ }
+
+ private void assertDirectory(DownloadedFile actual, String expectedPath)
+ {
+ assertEquals(expectedPath, actual.file.getPath());
+ assertEquals(true, actual.file.isDirectory());
+ assertEquals(0, actual.file.getFileLength());
+ assertEquals("", actual.content);
+ }
+
+ private void assertFile(DownloadedFile actual, String expectedPath, String expectedFileContent)
+ {
+ assertEquals(expectedPath, actual.file.getPath());
+ assertEquals(false, actual.file.isDirectory());
+ assertEquals(expectedFileContent.length(), actual.file.getFileLength());
+ assertEquals(expectedFileContent, actual.content);
+ }
+
+ private void assertResponseOK(ContentResponse response)
+ {
+ int statusCode = response.getStatus();
+ if (statusCode != HttpStatus.Code.OK.getCode())
+ {
+ throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
+ }
+ }
+
+ private void assertResponseError(ContentResponse response)
+ {
+ int statusCode = response.getStatus();
+ if (statusCode != HttpStatus.Code.INTERNAL_SERVER_ERROR.getCode())
+ {
+ throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.INTERNAL_SERVER_ERROR.getCode());
+ }
+ }
+
+ private class FileToUpload
+ {
+ private String fieldName;
+
+ private String fileName;
+
+ private String content;
+
+ public FileToUpload()
+ {
+ this("testFieldName", "testFileName", "testContent");
+ }
+
+ public FileToUpload(String fieldName, String fileName, String content)
+ {
+ this.fieldName = fieldName;
+ this.fileName = fileName;
+ this.content = content;
+ }
+ }
+
+ private class DownloadedFile
+ {
+ private DataSetFile file;
+
+ private String content;
+
+ public DownloadedFile(DataSetFile file, String content)
+ {
+ this.file = file;
+ this.content = content;
+ }
+
+ }
+
+}
diff --git a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/UploadAndCreateDataSetsTest.java b/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/UploadAndCreateDataSetsTest.java
deleted file mode 100644
index 6cce8c6c82eeee7180f860e56b048402cb2f7fc8..0000000000000000000000000000000000000000
--- a/datastore_server/sourceTest/java/ch/ethz/sis/openbis/generic/dss/systemtest/api/v3/UploadAndCreateDataSetsTest.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Copyright 2017 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.dss.systemtest.api.v3;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.MalformedURLException;
-import java.util.Arrays;
-import java.util.List;
-import java.util.UUID;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-
-import org.eclipse.jetty.client.HttpClient;
-import org.eclipse.jetty.client.api.ContentProvider;
-import org.eclipse.jetty.client.api.ContentResponse;
-import org.eclipse.jetty.client.api.Request;
-import org.eclipse.jetty.client.util.StringContentProvider;
-import org.eclipse.jetty.http.HttpStatus;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.CreationId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.PhysicalDataCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.FileFormatTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.ProprietaryStorageFormatPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.RelativeLocationLocatorTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentIdentifier;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.FullDataSetCreation;
-import ch.ethz.sis.openbis.generic.server.dssapi.v3.upload.StoreShareFileUploadServlet;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.util.TestInstanceHostUtils;
-
-/**
- * @author Ganime Betul Akin
- */
-public class UploadAndCreateDataSetsTest extends AbstractFileTest
-{
- private static final String SERVICE_URL = TestInstanceHostUtils.getDSSUrl() + "/datastore_server/"
- + "store_share_file_upload";
-
- protected StoreShareFileUploadServlet servlet;
-
- protected String sessionToken;
-
- protected static final String UNIT_TEST_WORKING_DIRECTORY = "unit-test-wd";
-
- protected static final String TARGETS_DIRECTORY = "targets";
-
- protected static final File UNIT_TEST_ROOT_DIRECTORY = new File(TARGETS_DIRECTORY
- + File.separator + UNIT_TEST_WORKING_DIRECTORY);
-
- /**
- * Create a dummy file of size <code>length</code> bytes.
- */
- private File createDummyFile(File dir, String name, int length) throws IOException
- {
- File dummyFile = new File(dir, name);
- dummyFile.createNewFile();
- PrintWriter out = new PrintWriter(dummyFile);
- for (int i = 0; i < length; ++i)
- {
- out.append('a');
- }
- out.flush();
- out.close();
-
- return dummyFile;
- }
-
- @Test
- public void testFileUpload()
- {
- HttpClient client = JettyHttpClientFactory.getHttpClient();
- Request requestEntity = client.newRequest(SERVICE_URL).method("POST");
-
- String sessionToken = gis.tryToAuthenticateForAllServices(TEST_USER, PASSWORD);
-
- String uploadId = "1357";
- requestEntity.param("uploadID", uploadId);
- String dataSetType = "UNKNOWN";
- requestEntity.param("dataSetType", dataSetType);
- requestEntity.param("sessionID", sessionToken);
-
- final String CRLF = "\r\n";
- final String BOUNDARY = "MMMMM___MP_BOUNDARY___MMMMM";
- final String FILE_PART_NAME = "fastaFile";
-
- File fileToUpload;
- try
- {
- fileToUpload = createDummyFile(workingDirectory, "to-upload.txt", 80);
- String fileContent = FileUtilities.loadToString(fileToUpload);
- ContentProvider content = new StringContentProvider("--" + BOUNDARY + CRLF
- + "Content-Disposition: form-data; name=\"" + FILE_PART_NAME + "\"; filename=\""
- + fileToUpload.getName() + "\"" + CRLF
- + "Content-Type: application/octet-stream" + CRLF + CRLF
- + fileContent + CRLF + "--" + BOUNDARY + "--" + CRLF);
- requestEntity.content(content, "multipart/form-data; boundary=" + BOUNDARY);
-
- ContentResponse contentResponse;
- contentResponse = requestEntity.send();
- int statusCode = contentResponse.getStatus();
-
- if (statusCode != HttpStatus.Code.OK.getCode())
- {
- throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
- }
-
- DataSetCreation metadataCreation = new DataSetCreation();
- metadataCreation.setTypeId(new EntityTypePermId(dataSetType));
- metadataCreation.setDataSetKind(DataSetKind.PHYSICAL);;
- metadataCreation.setAutoGeneratedCode(true);
- metadataCreation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
- metadataCreation.setDataStoreId(new DataStorePermId("STANDARD"));
- metadataCreation.setCreationId(new CreationId(uploadId));
-
- String code = UUID.randomUUID().toString();
- PhysicalDataCreation physicalCreation = new PhysicalDataCreation();
- physicalCreation.setLocation("test/location/" + code);
- physicalCreation.setFileFormatTypeId(new FileFormatTypePermId("TIFF"));
- physicalCreation.setLocatorTypeId(new RelativeLocationLocatorTypePermId());
- physicalCreation.setStorageFormatId(new ProprietaryStorageFormatPermId());
-
- metadataCreation.setPhysicalData(physicalCreation);
- FullDataSetCreation newDataSet = new FullDataSetCreation();
-
- newDataSet.setMetadataCreation(metadataCreation);
- List<DataSetPermId> createDataSets = dss.createDataSets(sessionToken, Arrays.asList(newDataSet));
- } catch (InterruptedException | TimeoutException | ExecutionException | IOException e)
- {
- e.printStackTrace();
- }
- }
-
- @BeforeMethod
- public void beforeMethod() throws MalformedURLException
- {
- }
-}
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
index dfb0e81c8e69168b0bd20b052a08a13b28cc1e10..3cba9b37164c7bfad7dccf506ed4a320037c1b6c 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/common.js
@@ -39,6 +39,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
this.SemanticAnnotationCreation = dtos.SemanticAnnotationCreation;
this.DataSetCreation = dtos.DataSetCreation;
this.FullDataSetCreation = dtos.FullDataSetCreation;
+ this.UploadedDataSetCreation = dtos.UploadedDataSetCreation;
this.DataSetFileCreation = dtos.DataSetFileCreation;
this.LinkedDataCreation = dtos.LinkedDataCreation;
this.ContentCopyCreation = dtos.ContentCopyCreation;
@@ -163,6 +164,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
this.DataSetTypeCreation = dtos.DataSetTypeCreation;
this.MaterialTypeCreation = dtos.MaterialTypeCreation;
this.PropertyTypeCreation = dtos.PropertyTypeCreation;
+ this.PropertyTypeUpdate = dtos.PropertyTypeUpdate;
this.WebAppSettings = dtos.WebAppSettings;
// operations
@@ -214,6 +216,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
this.UpdateDataSetTypesOperation = dtos.UpdateDataSetTypesOperation;
this.UpdateMaterialsOperation = dtos.UpdateMaterialsOperation;
this.UpdateMaterialTypesOperation = dtos.UpdateMaterialTypesOperation;
+ this.UpdatePropertyTypesOperation = dtos.UpdatePropertyTypesOperation;
this.UpdateVocabulariesOperation = dtos.UpdateVocabulariesOperation;
this.UpdateVocabularyTermsOperation = dtos.UpdateVocabularyTermsOperation;
this.UpdateExternalDmsOperation = dtos.UpdateExternalDmsOperation;
@@ -294,7 +297,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
this.getDtos = function() {
return dtos;
}
-
+
this.getId = function(entity) {
if (typeof entity["getPermId"] === 'function') {
return entity.getPermId();
@@ -389,6 +392,33 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
});
}.bind(this);
+ this.waitUntilIndexed = function(facade, dataSetCode, timeout) {
+ var c = this;
+ var dfd = $.Deferred();
+ var start = new Date().getTime();
+
+ var searchAndWait = function() {
+ var criteria = new c.DataSetSearchCriteria();
+ criteria.withPermId().thatEquals(dataSetCode);
+
+ facade.searchDataSets(criteria, c.createDataSetFetchOptions()).then(function(result) {
+ if (result.getTotalCount() == 0) {
+ var now = new Date().getTime();
+ if (now - start > timeout) {
+ c.fail("Data set " + dataSetCode + " not indexed after " + timeout + " msec.");
+ dfd.reject();
+ } else {
+ setTimeout(searchAndWait, 1000);
+ }
+ } else {
+ dfd.resolve();
+ }
+ });
+ };
+ searchAndWait();
+ return dfd.promise();
+ }.bind(this);
+
this.getResponseFromJSTestAggregationService = function(facade, params, callback) {
var c = this;
return $.ajax({
@@ -454,7 +484,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
return permIds[0];
});
}.bind(this);
-
+
this.createExternalDms = function(facade) {
var c = this;
var creation = new dtos.ExternalDmsCreation();
@@ -491,12 +521,12 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
var c = this;
var creation = new dtos.AuthorizationGroupCreation();
creation.setCode(c.generateId("AUTHORIZATION_GROUP"));
- creation.setUserIds([new c.PersonPermId("power_user")]);
+ creation.setUserIds([ new c.PersonPermId("power_user") ]);
return facade.createAuthorizationGroups([ creation ]).then(function(permIds) {
return permIds[0];
});
}.bind(this);
-
+
this.createRoleAssignment = function(facade, isUser) {
var c = this;
return c.createSpace(facade).then(function(spaceId) {
@@ -513,7 +543,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
});
});
}.bind(this);
-
+
this.createPerson = function(facade) {
var c = this;
var creation = new dtos.PersonCreation();
@@ -522,7 +552,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
return permIds[0];
});
}.bind(this);
-
+
this.createSemanticAnnotation = function(facade) {
var c = this;
var creation = new dtos.SemanticAnnotationCreation();
@@ -662,14 +692,14 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
return groups[id];
});
}.bind(this);
-
+
this.findRoleAssignment = function(facade, id) {
var c = this;
return facade.getRoleAssignments([ id ], c.createRoleAssignmentFetchOptions()).then(function(assignments) {
return assignments[id];
});
}.bind(this);
-
+
this.findPerson = function(facade, id) {
var c = this;
return facade.getPersons([ id ], c.createPersonFetchOptions()).then(function(persons) {
@@ -767,7 +797,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
options.setReason("test reason");
return facade.deleteVocabularyTerms([ id ], options);
}.bind(this);
-
+
this.replaceVocabularyTerm = function(facade, id) {
var c = this;
var options = new dtos.VocabularyTermDeletionOptions();
@@ -789,14 +819,14 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
options.setReason("test reason");
return facade.deleteAuthorizationGroups([ id ], options);
}.bind(this);
-
+
this.deleteRoleAssignment = function(facade, id) {
var c = this;
var options = new dtos.RoleAssignmentDeletionOptions();
options.setReason("test reason");
return facade.deleteRoleAssignments([ id ], options);
}.bind(this);
-
+
this.deleteOperationExecution = function(facade, id) {
var c = this;
var options = new dtos.OperationExecutionDeletionOptions();
@@ -1009,7 +1039,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
rafo.withProject().withSpace();
return fo;
};
-
+
this.createRoleAssignmentFetchOptions = function() {
var fo = new dtos.RoleAssignmentFetchOptions();
fo.withProject();
@@ -1019,7 +1049,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
fo.withRegistrator();
return fo;
};
-
+
this.createPersonFetchOptions = function() {
var fo = new dtos.PersonFetchOptions();
fo.withSpace();
@@ -1027,7 +1057,7 @@ define([ 'jquery', 'openbis', 'underscore', 'test/dtos' ], function($, defaultOp
fo.withRegistrator();
return fo;
};
-
+
this.createPropertyTypeFetchOptions = function() {
var fo = new dtos.PropertyTypeFetchOptions();
fo.withVocabulary();
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
index 808675c41aba52a2a539becd4b13a2a1d361619a..9ff3f5104471536f23e7ece872a9b0a7130c288d 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/dtos.js
@@ -444,6 +444,9 @@ var sources = [
'as/dto/property/search/SearchPropertyTypesOperationResult',
'as/dto/property/search/SearchPropertyAssignmentsOperation',
'as/dto/property/search/SearchPropertyAssignmentsOperationResult',
+ 'as/dto/property/update/PropertyTypeUpdate',
+ 'as/dto/property/update/UpdatePropertyTypesOperation',
+ 'as/dto/property/update/UpdatePropertyTypesOperationResult',
'as/dto/property/DataType',
'as/dto/property/PropertyAssignment',
'as/dto/property/PropertyType',
@@ -656,6 +659,7 @@ var sources = [
'as/dto/operation/SynchronousOperationExecutionResults',
'dss/dto/dataset/create/FullDataSetCreation',
+ 'dss/dto/dataset/create/UploadedDataSetCreation',
'dss/dto/datasetfile/DataSetFile',
'dss/dto/datasetfile/create/DataSetFileCreation',
'dss/dto/datasetfile/fetchoptions/DataSetFileSortOptions',
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
index 5668c4070c021a96584cdbaa9ddf5f62340e2d28..f7e4492e041191e5000331f2dec890cdfed8e731 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/openbis-execute-operations.js
@@ -205,6 +205,10 @@ define([ 'jquery', 'openbis', 'test/common' ], function($, openbis, common) {
return this._executeUpdateOperation(new c.UpdateVocabulariesOperation(updates));
}
+ this.updatePropertyTypes = function(updates) {
+ return this._executeUpdateOperation(new c.UpdatePropertyTypesOperation(updates));
+ }
+
this.updateVocabularyTerms = function(updates) {
return this._executeUpdateOperation(new c.UpdateVocabularyTermsOperation(updates));
}
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
index 7c6298b5f4dbc8fa7531a925899dfa31120f4b0a..fb9a6faa84a93f856b8830718fa9156412608f1a 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-create.js
@@ -295,23 +295,6 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
});
}
- var waitUntilIndexed = function(facade, dataSetCode, timeout, action) {
- if (timeout < 0) {
- c.fail("Data set " + dataSetCode + " after " + timeout + " msec.");
- }
- setTimeout(function() {
- var criteria = new c.DataSetSearchCriteria();
- criteria.withPermId().thatEquals(dataSetCode);
- facade.searchDataSets(criteria, c.createDataSetFetchOptions()).then(function(result) {
- if (result.getTotalCount() == 0) {
- waitUntilIndexed(facade, dataSetCode, timeout - 1000, action);
- } else {
- action();
- }
- });
- }, 1000)
- };
-
var fCheck = function(dataSet, facade) {
c.assertEqual(dataSet.getType().getCode(), "LINK_TYPE", "Data set type");
var contentCopies = dataSet.getLinkedData().getContentCopies();
@@ -321,7 +304,7 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
c.assertEqual(contentCopy.getPath(), "/my/path", "Content copy path");
var dfd = $.Deferred()
var dataSetCode = dataSet.getCode();
- waitUntilIndexed(facade, dataSetCode, 10000, function() {
+ c.waitUntilIndexed(facade, dataSetCode, 10000).then(function() {
var criteria = new c.DataSetFileSearchCriteria();
criteria.withDataSet().withCode().thatEquals(dataSet.getCode());
facade.getDataStoreFacade("DSS1").searchFiles(criteria, c.createDataSetFileFetchOptions()).then(function(result) {
@@ -506,7 +489,7 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
vocabularyCreation.setUrlTemplate("https://www.ethz.ch");
var termCreation = new c.VocabularyTermCreation();
termCreation.setCode("alpha");
- vocabularyCreation.setTerms([termCreation]);
+ vocabularyCreation.setTerms([ termCreation ]);
return facade.createVocabularies([ vocabularyCreation ]);
}
@@ -525,7 +508,7 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
QUnit.test("createVocabularyTerms()", function(assert) {
var c = new common(assert, openbis);
var code = c.generateId("VOCABULARY_TERM");
-
+
var fCreate = function(facade) {
var termCreation = new c.VocabularyTermCreation();
termCreation.setVocabularyId(new c.VocabularyPermId("TEST-VOCABULARY"));
@@ -536,7 +519,7 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
termCreation.setPreviousTermId(new c.VocabularyTermPermId("TEST-TERM-1", "TEST-VOCABULARY"))
return facade.createVocabularyTerms([ termCreation ]);
}
-
+
var fCheck = function(term) {
c.assertEqual(term.getCode(), code, "Term code");
c.assertEqual(term.getVocabulary().getCode(), "TEST-VOCABULARY", "Term vocabulary code");
@@ -545,10 +528,10 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
c.assertEqual(term.isOfficial(), true, "Term official");
c.assertEqual(term.getOrdinal(), 2, "Term ordinal");
}
-
+
testCreate(c, fCreate, c.findVocabularyTerm, fCheck);
});
-
+
QUnit.test("createExternalDataManagementSystem()", function(assert) {
var c = new common(assert, openbis);
var code = c.generateId("EDMS");
@@ -598,15 +581,15 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
var c = new common(assert, openbis);
var code = c.generateId("AUTHORIZATION_GROUP");
var description = "Description of " + code;
-
+
var fCreate = function(facade) {
var creation = new c.AuthorizationGroupCreation();
creation.setCode(code);
creation.setDescription(description);
- creation.setUserIds([new c.PersonPermId("power_user")]);
+ creation.setUserIds([ new c.PersonPermId("power_user") ]);
return facade.createAuthorizationGroups([ creation ]);
}
-
+
var fCheck = function(group) {
c.assertEqual(group.getCode(), code, "Code");
c.assertEqual(group.getDescription(), description, "Description");
@@ -616,54 +599,54 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
users.sort();
c.assertEqual(users.toString(), "power_user", "Users");
}
-
+
testCreate(c, fCreate, c.findAuthorizationGroup, fCheck);
});
-
+
QUnit.test("createRoleAssignments() for space user", function(assert) {
var c = new common(assert, openbis);
-
+
var fCreate = function(facade) {
return c.createSpace(facade).then(function(spaceId) {
var creation = new c.RoleAssignmentCreation();
creation.setRole(c.Role.POWER_USER);
creation.setUserId(new c.PersonPermId("power_user"));
creation.setSpaceId(spaceId);
- return facade.createRoleAssignments([creation]);
+ return facade.createRoleAssignments([ creation ]);
});
}
-
+
var fCheck = function(roleAssignment) {
c.assertEqual(roleAssignment.getUser().getUserId(), "power_user", "User");
c.assertEqual(roleAssignment.getRole(), c.Role.POWER_USER, "Role");
c.assertEqual(roleAssignment.getRoleLevel(), c.RoleLevel.SPACE, "Role level");
c.assertEqual(roleAssignment.getRegistrator().getUserId(), "openbis_test_js", "Registrator");
}
-
+
testCreate(c, fCreate, c.findRoleAssignment, fCheck);
});
-
+
QUnit.test("createPersons()", function(assert) {
var c = new common(assert, openbis);
var userId = c.generateId("user");
-
+
var fCreate = function(facade) {
var personCreation = new c.PersonCreation();
personCreation.setUserId(userId);
personCreation.setHomeSpaceId(new c.SpacePermId("TEST"))
return facade.createPersons([ personCreation ]);
}
-
+
var fCheck = function(person) {
c.assertEqual(person.getUserId(), userId, "User id");
c.assertEqual(person.getRegistrator().getUserId(), "openbis_test_js", "Registrator");
c.assertEqual(person.isActive(), true, "User active");
c.assertEqual(person.getSpace().getCode(), "TEST", "Home space");
}
-
+
testCreate(c, fCreate, c.findPerson, fCheck);
});
-
+
var createSemanticAnnotationCreation = function(c) {
var creation = new c.SemanticAnnotationCreation();
creation.setPredicateOntologyId("jsPredicateOntologyId");
@@ -737,6 +720,71 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
testCreate(c, fCreate, c.findSemanticAnnotation, fCheck);
});
+ QUnit.test("createUploadedDataSet()", function(assert) {
+ var c = new common(assert, openbis);
+
+ var fCreate = function(facade) {
+
+ // unfortunately old Firefox that is used together with our
+ // Selenium tests does not allow to use FormData class which
+ // would make constructing form data much easier
+
+ var formData = "------WebKitFormBoundary7MA4YWxkTrZu0gW\r\nContent-Disposition: form-data; name=\"file\"; filename=\"file1.txt\"\r\nContent-Type: text/plain\r\n\r\n\r\ncontent1\r\n"
+ + "------WebKitFormBoundary7MA4YWxkTrZu0gW\r\nContent-Disposition: form-data; name=\"file\"; filename=\"file2.txt\"\r\nContent-Type: text/plain\r\n\r\n\r\ncontent2\r\n"
+ + "------WebKitFormBoundary7MA4YWxkTrZu0gW--";
+
+ var dataStoreFacade = facade.getDataStoreFacade("DSS1");
+
+ return dataStoreFacade.createDataSetUpload("UNKNOWN").then(function(upload) {
+ return $.ajax({
+ url : upload.url,
+ type : "POST",
+ processData : false,
+ contentType : "multipart/form-data; boundary=----WebKitFormBoundary7MA4YWxkTrZu0gW",
+ data : formData
+ }).then(function() {
+ return c.createExperiment(facade).then(function(experimentPermId) {
+ var creation = new c.UploadedDataSetCreation();
+ creation.setUploadId(upload.id);
+ creation.setTypeId(new c.EntityTypePermId(upload.dataSetType));
+ creation.setExperimentId(experimentPermId);
+ creation.setProperty("DESCRIPTION", "test description");
+ creation.setParentIds([ new c.DataSetPermId("20130424111751432-431") ]);
+ return dataStoreFacade.createUploadedDataSet(creation).then(function(permId) {
+ return [ permId ];
+ })
+ });
+ });
+ });
+ }
+
+ var fCheck = function(dataSet, facade) {
+ return c.waitUntilIndexed(facade, dataSet.getCode(), 10000).then(function() {
+ var dataStoreFacade = facade.getDataStoreFacade("DSS1");
+
+ var criteria = new c.DataSetFileSearchCriteria();
+ criteria.withDataSet().withCode().thatEquals(dataSet.getCode());
+
+ return dataStoreFacade.searchFiles(criteria, c.createDataSetFileFetchOptions()).then(function(result) {
+ var files = result.getObjects();
+ c.assertEqual(files.length, 5, "Number of files");
+ c.assertEqual(files[0].path, "", "Path 0");
+ c.assertEqual(files[1].path, "original", "Path 1");
+ c.assertEqual(files[2].path, "original/upload", "Path 2");
+ c.assertEqual(files[3].path, "original/upload/file1.txt", "Path 3");
+ c.assertEqual(files[4].path, "original/upload/file2.txt", "Path 4");
+
+ c.assertEqual(dataSet.getType().getCode(), "UNKNOWN", "Type code");
+ c.assertEqual(dataSet.getProperty("DESCRIPTION"), "test description", "'DESCRIPTION' property value");
+ c.assertEqual(dataSet.getParents().length, 1, "Number of parents");
+ c.assertEqual(dataSet.getParents()[0].getCode(), "20130424111751432-431", "Parent code");
+ });
+ });
+ }
+
+ testCreate(c, fCreate, c.findDataSet, fCheck);
+ });
+
}
return function() {
diff --git a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-update.js b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-update.js
index a84aebb8780f162ab1ccc7f243ceba7ea1c85e12..94d3b4f57b0642bafa031431646977868a275afb 100644
--- a/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-update.js
+++ b/js-test/servers/common/core-plugins/tests/1/as/webapps/openbis-v3-api-test/html/test/test-update.js
@@ -705,17 +705,49 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
testUpdate(c, fCreate, fUpdate, c.findMaterial, fCheck);
});
+ QUnit.test("updatePropertyTypes()", function(assert) {
+ var c = new common(assert, openbis);
+ var code = c.generateId("PROPERTY_TYPE");
+ var description = "Description of " + code;
+ var label = "Label of " + code;
+
+ var fCreate = function(facade) {
+ var creation = new c.PropertyTypeCreation();
+ creation.setCode(code);
+ creation.setLabel("Testing");
+ creation.setDescription("testing");
+ creation.setDataType(c.DataType.VARCHAR);
+ return facade.createPropertyTypes([ creation ]);
+ }
+
+ var fUpdate = function(facade, permId) {
+ var update = new c.PropertyTypeUpdate();
+ update.setTypeId(new c.PropertyTypePermId(code));
+ update.setDescription(description);
+ update.setLabel(label);
+ return facade.updatePropertyTypes([ update ]);
+ }
+
+ var fCheck = function(propertyType) {
+ c.assertEqual(propertyType.getCode(), code, "Code");
+ c.assertEqual(propertyType.getDescription(), description, "Description");
+ c.assertEqual(propertyType.getLabel(), label, "Label");
+ }
+
+ testUpdate(c, fCreate, fUpdate, c.findPropertyType, fCheck);
+ });
+
QUnit.test("updateVocabularies()", function(assert) {
var c = new common(assert, openbis);
var code = c.generateId("VOCABULARY");
var description = "Description of " + code;
-
+
var fCreate = function(facade) {
var creation = new c.VocabularyCreation();
creation.setCode(code);
return facade.createVocabularies([ creation ]);
}
-
+
var fUpdate = function(facade, permId) {
var update = new c.VocabularyUpdate();
update.setVocabularyId(permId);
@@ -724,14 +756,14 @@ define([ 'jquery', 'underscore', 'openbis', 'test/openbis-execute-operations', '
update.setUrlTemplate("https://www.ethz.ch")
return facade.updateVocabularies([ update ]);
}
-
+
var fCheck = function(vocabulary) {
c.assertEqual(vocabulary.getCode(), code, "Code");
c.assertEqual(vocabulary.getPermId().getPermId(), code, "Perm id");
c.assertEqual(vocabulary.getDescription(), description, "Description");
c.assertEqual(vocabulary.getUrlTemplate(), "https://www.ethz.ch", "URL template");
}
-
+
testUpdate(c, fCreate, fUpdate, c.findVocabulary, fCheck);
});
diff --git a/js-test/servers/common/datastore_server/etc/service.properties b/js-test/servers/common/datastore_server/etc/service.properties
index ce0ee81e53d5bf8feb58240e47f3f55c5d4ab83d..a4f556253edf350dcab9eb055c264f4528829979 100644
--- a/js-test/servers/common/datastore_server/etc/service.properties
+++ b/js-test/servers/common/datastore_server/etc/service.properties
@@ -148,7 +148,7 @@ default-dropbox.incoming-data-completeness-condition = auto-detection
default-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2
default-dropbox.program-class = ch.systemsx.cisd.etlserver.registrator.DefaultDropbox
default-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-default-dropbox.validation-script-path = ../core-plugins/default/default-validation-script.py
+#default-dropbox.validation-script-path = ../core-plugins/default/default-validation-script.py
# ---------------------------------------------------------------------------
# Archiver configuration (optional)
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
index 066fe6346b9627d19bd1095e0a97933635586c17..fb2601743794209c69a6ee31bd4d84d5ac54b33b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApi.java
@@ -235,6 +235,8 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.SearchPropertyAs
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.SearchPropertyAssignmentsOperationResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.SearchPropertyTypesOperation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.SearchPropertyTypesOperationResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.UpdatePropertyTypesOperation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.RoleAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create.CreateRoleAssignmentsOperation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create.CreateRoleAssignmentsOperationResult;
@@ -658,6 +660,12 @@ public class ApplicationServerApi extends AbstractServer<IApplicationServerApi>
executeOperation(sessionToken, new UpdateDataSetTypesOperation(dataSetTypeUpdates));
}
+ @Override
+ public void updatePropertyTypes(String sessionToken, List<PropertyTypeUpdate> propertyTypeUpdates)
+ {
+ executeOperation(sessionToken, new UpdatePropertyTypesOperation(propertyTypeUpdates));
+ }
+
@Override
public void updateVocabularies(String sessionToken, List<VocabularyUpdate> vocabularyUpdates)
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
index 7aa5e6ba88544cbbe6ebc671fa982a9b5df855a4..fbbf22a2c5f017f8008b0d4b6a34bdbb5fb38703 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/ApplicationServerApiLogger.java
@@ -127,6 +127,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyAssignmentSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.RoleAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create.RoleAssignmentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.delete.RoleAssignmentDeletionOptions;
@@ -436,6 +437,12 @@ public class ApplicationServerApiLogger extends AbstractServerLogger implements
logAccess(sessionToken, "update-material-types", "MATERIAL_TYPE_UPDATES(%s)", abbreviate(materialTypeUpdates));
}
+ @Override
+ public void updatePropertyTypes(String sessionToken, List<PropertyTypeUpdate> propertyTypeUpdates)
+ {
+ logAccess(sessionToken, "update-property_types", "PROPERTY_TYPE_UPDATES(%s)", abbreviate(propertyTypeUpdates));
+ }
+
@Override
public void updateVocabularies(String sessionToken, List<VocabularyUpdate> vocabularyUpdates)
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractUpdateEntityExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractUpdateEntityExecutor.java
index 684a413662019b0db4e154ab79a7179d164de4d7..b6dce6196377a1bd4fb6ce9576ea052e521ba7fd 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractUpdateEntityExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/entity/AbstractUpdateEntityExecutor.java
@@ -31,6 +31,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.dao.DataAccessException;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.id.IObjectId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.FieldUpdateValue;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.IUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.ObjectNotFoundException;
import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.UnauthorizedObjectAccessException;
@@ -216,6 +217,12 @@ public abstract class AbstractUpdateEntityExecutor<UPDATE extends IUpdate, PE ex
entry.setValue(idToEntityMap.get(entry.getValue().getId()));
}
}
+
+ protected <T> T getNewValue(FieldUpdateValue<T> fieldUpdateValue, T currentValue)
+ {
+ return fieldUpdateValue != null && fieldUpdateValue.isModified() ? fieldUpdateValue.getValue() : currentValue;
+ }
+
protected abstract ID getId(UPDATE update);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
index 662c18b6cb6d2b4f060a57bbc2c0292d16f6d200..f45065bca3b00d235a08c1a7fca961e0487ee8a8 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/operation/OperationsExecutor.java
@@ -91,6 +91,7 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property.ICreateProp
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property.IGetPropertyTypesOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property.ISearchPropertyAssignmentsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property.ISearchPropertyTypesOperationExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property.IUpdatePropertyTypesOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.roleassignment.ICreateRoleAssignmentsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.roleassignment.IDeleteRoleAssignmentsOperationExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.roleassignment.IGetRoleAssignmentsOperationExecutor;
@@ -287,6 +288,9 @@ public class OperationsExecutor implements IOperationsExecutor
@Autowired
private IUpdateExternalDmsOperationExecutor updateExternalDmsExecutor;
+
+ @Autowired
+ private IUpdatePropertyTypesOperationExecutor updatePropertyTypesExecutor;
@Autowired
private IUpdateVocabulariesOperationExecutor updateVocabulariesExecutor;
@@ -574,6 +578,7 @@ public class OperationsExecutor implements IOperationsExecutor
resultMap.putAll(updateSemanticAnnotationsExecutor.execute(context, operations));
resultMap.putAll(updateOperationExecutionsExecutor.execute(context, operations));
resultMap.putAll(updateVocabulariesExecutor.execute(context, operations));
+ resultMap.putAll(updatePropertyTypesExecutor.execute(context, operations));
resultMap.putAll(updateVocabularyTermsExecutor.execute(context, operations));
resultMap.putAll(updateMaterialTypesExecutor.execute(context, operations));
resultMap.putAll(updateExperimentTypesExecutor.execute(context, operations));
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IPropertyTypeAuthorizationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IPropertyTypeAuthorizationExecutor.java
index b148bd599f159af8e15e346cf52430c7b67c6466..6ad43d9802fe62aa847b7855f9d7f0017e148f69 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IPropertyTypeAuthorizationExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IPropertyTypeAuthorizationExecutor.java
@@ -16,8 +16,10 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.IObjectAuthorizationExecutor;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
/**
* @author pkupczyk
@@ -31,4 +33,6 @@ public interface IPropertyTypeAuthorizationExecutor extends IObjectAuthorization
void canCreate(IOperationContext context);
+ void canUpdate(IOperationContext context, IPropertyTypeId id, PropertyTypePE entity);
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypeExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..b99b9747f6c43f91da7ac8af52500d3dcdba17f2
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypeExecutor.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2018 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.asapi.v3.executor.property;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.IUpdateEntityExecutor;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+public interface IUpdatePropertyTypeExecutor extends IUpdateEntityExecutor<PropertyTypeUpdate, PropertyTypePermId>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypesOperationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypesOperationExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..1d9a496a7092b6626c475fabab0790e3f26ca32f
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/IUpdatePropertyTypesOperationExecutor.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright 2018 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.asapi.v3.executor.property;
+
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.update.IUpdateObjectsOperationExecutor;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+public interface IUpdatePropertyTypesOperationExecutor extends IUpdateObjectsOperationExecutor
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/PropertyTypeAuthorizationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/PropertyTypeAuthorizationExecutor.java
index 163f86d9fae3adbe44ee7da7f57ca7581c55810d..8626d432c8140def7dabbc14c6f66e4d520db720 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/PropertyTypeAuthorizationExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/PropertyTypeAuthorizationExecutor.java
@@ -18,10 +18,12 @@ package ch.ethz.sis.openbis.generic.server.asapi.v3.executor.property;
import org.springframework.stereotype.Component;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.Capability;
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.generic.shared.dto.PropertyTypePE;
/**
* @author pkupczyk
@@ -51,4 +53,11 @@ public class PropertyTypeAuthorizationExecutor implements IPropertyTypeAuthoriza
{
}
+ @Override
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_ADMIN)
+ @Capability("UPDATE_PROPERTY_TYPE")
+ public void canUpdate(IOperationContext context, IPropertyTypeId id, PropertyTypePE entity)
+ {
+ }
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypeExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..deb11b335c0778ae009289e1e77ee7646fbe50ea
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypeExecutor.java
@@ -0,0 +1,143 @@
+/*
+ * Copyright 2018 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.asapi.v3.executor.property;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import org.apache.commons.lang.StringUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DataAccessException;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.AbstractUpdateEntityExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.common.batch.MapBatch;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.util.XmlUtils;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+@Component
+public class UpdatePropertyTypeExecutor
+ extends AbstractUpdateEntityExecutor<PropertyTypeUpdate, PropertyTypePE, IPropertyTypeId, PropertyTypePermId>
+ implements IUpdatePropertyTypeExecutor
+{
+ @Autowired
+ private IDAOFactory daoFactory;
+
+ @Autowired
+ private IMapPropertyTypeByIdExecutor mapPropertyTypeByIdExecutor;
+
+ @Autowired
+ private IPropertyTypeAuthorizationExecutor authorizationExecutor;
+
+ @Override
+ protected IPropertyTypeId getId(PropertyTypeUpdate update)
+ {
+ return update.getTypeId();
+ }
+
+ @Override
+ protected PropertyTypePermId getPermId(PropertyTypePE entity)
+ {
+ return new PropertyTypePermId(entity.getPermId());
+ }
+
+ @Override
+ protected void checkData(IOperationContext context, PropertyTypeUpdate update)
+ {
+ if (update.getTypeId() == null)
+ {
+ throw new UserFailureException("Property type id cannot be null.");
+ }
+ if (update.getLabel().isModified() && StringUtils.isEmpty(update.getLabel().getValue()))
+ {
+ throw new UserFailureException("Label cannot be empty.");
+ }
+ if (update.getDescription().isModified() && StringUtils.isEmpty(update.getDescription().getValue()))
+ {
+ throw new UserFailureException("Description cannot be empty.");
+ }
+ XmlUtils.validateXML(update.getSchema().getValue(), "XML Schema", XmlUtils.XML_SCHEMA_XSD_FILE_RESOURCE);
+ XmlUtils.validateXML(update.getTransformation().getValue(), "XSLT", XmlUtils.XSLT_XSD_FILE_RESOURCE);
+ }
+
+ @Override
+ protected void checkAccess(IOperationContext context, IPropertyTypeId id, PropertyTypePE entity)
+ {
+ authorizationExecutor.canUpdate(context, id, entity);
+ }
+
+ @Override
+ protected void updateBatch(IOperationContext context, MapBatch<PropertyTypeUpdate, PropertyTypePE> batch)
+ {
+ Set<Entry<PropertyTypeUpdate, PropertyTypePE>> entrySet = batch.getObjects().entrySet();
+ for (Entry<PropertyTypeUpdate, PropertyTypePE> entry : entrySet)
+ {
+ PropertyTypeUpdate update = entry.getKey();
+ PropertyTypePE propertyType = entry.getValue();
+ propertyType.setDescription(getNewValue(update.getDescription(), propertyType.getDescription()));
+ propertyType.setLabel(getNewValue(update.getLabel(), propertyType.getLabel()));
+ propertyType.setSchema(getNewValue(update.getSchema(), propertyType.getSchema()));
+ propertyType.setTransformation(getNewValue(update.getTransformation(), propertyType.getTransformation()));
+ }
+ }
+
+ @Override
+ protected void updateAll(IOperationContext context, MapBatch<PropertyTypeUpdate, PropertyTypePE> batch)
+ {
+ }
+
+ @Override
+ protected Map<IPropertyTypeId, PropertyTypePE> map(IOperationContext context, Collection<IPropertyTypeId> ids)
+ {
+ return mapPropertyTypeByIdExecutor.map(context, ids);
+ }
+
+ @Override
+ protected List<PropertyTypePE> list(IOperationContext context, Collection<Long> ids)
+ {
+ return daoFactory.getPropertyTypeDAO().listAllEntities();
+ }
+
+ @Override
+ protected void save(IOperationContext context, List<PropertyTypePE> entities, boolean clearCache)
+ {
+ for (PropertyTypePE propertyType : entities)
+ {
+ daoFactory.getPropertyTypeDAO().validateAndSaveUpdatedEntity(propertyType);
+ }
+ }
+
+ @Override
+ protected void handleException(DataAccessException e)
+ {
+ DataAccessExceptionTranslator.throwException(e, "property types", null);
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypesOperationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypesOperationExecutor.java
new file mode 100644
index 0000000000000000000000000000000000000000..6b7b5c579a9e8da1e444314bf5fb893670bd3c97
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/property/UpdatePropertyTypesOperationExecutor.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2018 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.asapi.v3.executor.property;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.UpdateObjectsOperation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.UpdateObjectsOperationResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.UpdatePropertyTypesOperation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.UpdatePropertyTypesOperationResult;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.update.UpdateObjectsOperationExecutor;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+@Component
+public class UpdatePropertyTypesOperationExecutor
+ extends UpdateObjectsOperationExecutor<PropertyTypeUpdate, IPropertyTypeId>
+ implements IUpdatePropertyTypesOperationExecutor
+{
+ @Autowired
+ private IUpdatePropertyTypeExecutor executor;
+
+ @Override
+ protected Class<? extends UpdateObjectsOperation<PropertyTypeUpdate>> getOperationClass()
+ {
+ return UpdatePropertyTypesOperation.class;
+ }
+
+ @Override
+ protected UpdateObjectsOperationResult<? extends IPropertyTypeId> doExecute(IOperationContext context,
+ UpdateObjectsOperation<PropertyTypeUpdate> operation)
+ {
+ return new UpdatePropertyTypesOperationResult(executor.update(context, operation.getUpdates()));
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/IUpdateVocabularyExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/IUpdateVocabularyExecutor.java
index a975bbc53e93e5f3f73696102136ae4425d94501..a8b6e34a85039314979517904efbd7f31c487158 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/IUpdateVocabularyExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/IUpdateVocabularyExecutor.java
@@ -26,5 +26,4 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.entity.IUpdateEntity
*/
public interface IUpdateVocabularyExecutor extends IUpdateEntityExecutor<VocabularyUpdate, VocabularyPermId>
{
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/UpdateVocabularyExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/UpdateVocabularyExecutor.java
index 79b1a700fa16ba089c37d26d3cedf5b33d69576f..d3a3b5e8fa2c214ee933c4bfbcae4bdfde9cdeea 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/UpdateVocabularyExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/executor/vocabulary/UpdateVocabularyExecutor.java
@@ -26,7 +26,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.dao.DataAccessException;
import org.springframework.stereotype.Component;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.FieldUpdateValue;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.IVocabularyId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.id.VocabularyPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.update.VocabularyUpdate;
@@ -96,11 +95,6 @@ public class UpdateVocabularyExecutor
}
}
- private <T> T getNewValue(FieldUpdateValue<T> fieldUpdateValue, T currentValue)
- {
- return fieldUpdateValue != null && fieldUpdateValue.isModified() ? fieldUpdateValue.getValue() : currentValue;
- }
-
@Override
protected void updateAll(IOperationContext context, MapBatch<VocabularyUpdate, VocabularyPE> batch)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
index 8f7c73228d5ee8a78a0052220d4db3333be6dcbb..58fa9e048e41f97db15ed61357a321d8b4d6e5cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
@@ -34,8 +35,11 @@ import javax.servlet.http.HttpServletRequest;
import org.apache.commons.collections4.CollectionUtils;
import org.springframework.beans.factory.annotation.Autowired;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.operation.IOperationResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.Complete;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.CreateDataSetsOperation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.CreateDataSetsOperationResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.LinkedDataCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.PhysicalDataCreation;
@@ -54,7 +58,7 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgressListener;
import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgressStack;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.OperationContext;
-import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.dataset.ICreateDataSetExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.IOperationsExecutor;
import ch.ethz.sis.openbis.generic.server.asapi.v3.helper.sample.ListSampleTechIdByIdentifier;
import ch.ethz.sis.openbis.generic.server.asapi.v3.utils.ExceptionUtils;
import ch.rinn.restrictions.Private;
@@ -334,7 +338,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
private IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
@Autowired
- private ICreateDataSetExecutor createDataSetExecutor;
+ private IOperationsExecutor operationsExecutor;
private long timeout = 5; // minutes
@@ -372,7 +376,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
IDataStoreServiceRegistrator dataStoreServiceRegistrator,
IDataStoreDataSourceManager dataSourceManager,
ISessionManager<Session> sessionManagerForEntityOperation,
- IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory, ICreateDataSetExecutor createDataSetExecutor)
+ IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory, IOperationsExecutor operationsExecutor)
{
super(authenticationService, sessionManager, daoFactory, propertiesBatchManager, boFactory);
this.daoFactory = daoFactory;
@@ -383,7 +387,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
this.dataSourceManager = dataSourceManager;
this.sessionManagerForEntityOperation = sessionManagerForEntityOperation;
this.managedPropertyEvaluatorFactory = managedPropertyEvaluatorFactory;
- this.createDataSetExecutor = createDataSetExecutor;
+ this.operationsExecutor = operationsExecutor;
}
@Override
@@ -2676,9 +2680,9 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
try
{
- List<DataSetPermId> ids = createDataSetExecutor.create(context, creations);
- daoFactory.getSessionFactory().getCurrentSession().flush();
- return ids.size();
+ CreateDataSetsOperation operation = new CreateDataSetsOperation(creations);
+ List<IOperationResult> results = operationsExecutor.execute(context, Arrays.asList(operation));
+ return ((CreateDataSetsOperationResult) results.get(0)).getObjectIds().size();
} catch (Throwable t)
{
throw ExceptionUtils.create(context, t);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
index 1324a52cd5c29f2b31e1a4874117c844fa494e43..37d75e0c22b4dc5960ddb48f3c9d3bc5e76c2b10 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/PropertyTypePE.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.common.collection.UnmodifiableSetDecorator;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentityHolder;
/**
* Persistence entity representing property type.
@@ -60,7 +61,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
{ @UniqueConstraint(columnNames =
{ ColumnNames.CODE_COLUMN, ColumnNames.IS_INTERNAL_NAMESPACE }) })
public final class PropertyTypePE extends HibernateAbstractRegistrationHolder implements
- Comparable<PropertyTypePE>, IIdAndCodeHolder
+ Comparable<PropertyTypePE>, IIdAndCodeHolder, IIdentityHolder
{
public static final PropertyTypePE[] EMPTY_ARRAY = new PropertyTypePE[0];
@@ -170,6 +171,20 @@ public final class PropertyTypePE extends HibernateAbstractRegistrationHolder im
return CodeConverter.tryToBusinessLayer(getSimpleCode(), isInternalNamespace());
}
+ @Override
+ @Transient
+ public String getIdentifier()
+ {
+ return getCode();
+ }
+
+ @Override
+ @Transient
+ public String getPermId()
+ {
+ return getCode();
+ }
+
@NotNull(message = ValidationMessages.DATA_TYPE_NOT_NULL_MESSAGE)
@ManyToOne(fetch = FetchType.EAGER)
@JoinColumn(name = ColumnNames.DATA_TYPE_COLUMN, updatable = false)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/PropertyTypeUpdate.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/PropertyTypeUpdate.js
new file mode 100644
index 0000000000000000000000000000000000000000..2b84f287d917780d732d03d667e89e01a8a59945
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/PropertyTypeUpdate.js
@@ -0,0 +1,54 @@
+define([ "stjs", "as/dto/common/update/FieldUpdateValue" ], function(stjs, FieldUpdateValue) {
+ var PropertyTypeUpdate = function() {
+ this.label = new FieldUpdateValue();
+ this.description = new FieldUpdateValue();
+ this.schema = new FieldUpdateValue();
+ this.transformation = new FieldUpdateValue();
+ };
+ stjs.extend(PropertyTypeUpdate, null, [], function(constructor, prototype) {
+ prototype['@type'] = 'as.dto.property.update.PropertyTypeUpdate';
+ constructor.serialVersionUID = 1;
+ prototype.typeId = null;
+ prototype.label = null;
+ prototype.description = null;
+ prototype.schema = null;
+ prototype.transformation = null;
+
+ prototype.getObjectId = function() {
+ return this.getTypeId();
+ };
+ prototype.getTypeId = function() {
+ return this.typeId;
+ };
+ prototype.setTypeId = function(typeId) {
+ this.typeId = typeId;
+ };
+ prototype.getLabel = function() {
+ return this.label;
+ };
+ prototype.setLabel = function(label) {
+ this.label.setValue(label);
+ };
+ prototype.getDescription = function() {
+ return this.description;
+ };
+ prototype.setDescription = function(description) {
+ this.description.setValue(description);
+ };
+ prototype.getSchema = function() {
+ return this.schema;
+ };
+ prototype.setSchema = function(schema) {
+ this.schema.setValue(schema);
+ };
+ prototype.getTransformation = function() {
+ return this.transformation;
+ };
+ prototype.setTransformation = function(transformation) {
+ this.transformation.setValue(transformation);
+ };
+ }, {
+ typeId : "IPropertyTypeId"
+ });
+ return PropertyTypeUpdate;
+})
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperation.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperation.js
new file mode 100644
index 0000000000000000000000000000000000000000..c10de1f330528058ca0062dccc2a781e02c1c788
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperation.js
@@ -0,0 +1,12 @@
+define([ "stjs", "as/dto/common/update/UpdateObjectsOperation" ], function(stjs, UpdateObjectsOperation) {
+ var UpdatePropertyTypesOperation = function(updates) {
+ UpdateObjectsOperation.call(this, updates);
+ };
+ stjs.extend(UpdatePropertyTypesOperation, UpdateObjectsOperation, [ UpdateObjectsOperation ], function(constructor, prototype) {
+ prototype['@type'] = 'as.dto.property.update.UpdatePropertyTypesOperation';
+ prototype.getMessage = function() {
+ return "UpdatePropertyTypesOperation";
+ };
+ }, {});
+ return UpdatePropertyTypesOperation;
+})
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperationResult.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperationResult.js
new file mode 100644
index 0000000000000000000000000000000000000000..1681b61c4faf779162f596febaa0f3e0ba19e6f2
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/as/dto/property/update/UpdatePropertyTypesOperationResult.js
@@ -0,0 +1,12 @@
+define([ "stjs", "as/dto/common/update/UpdateObjectsOperationResult" ], function(stjs, UpdateObjectsOperationResult) {
+ var UpdatePropertyTypesOperationResult = function(objectIds) {
+ UpdateObjectsOperationResult.call(this, objectIds);
+ };
+ stjs.extend(UpdatePropertyTypesOperationResult, UpdateObjectsOperationResult, [ UpdateObjectsOperationResult ], function(constructor, prototype) {
+ prototype['@type'] = 'as.dto.property.update.UpdatePropertyTypesOperationResult';
+ prototype.getMessage = function() {
+ return "UpdatePropertyTypesOperationResult";
+ };
+ }, {});
+ return UpdatePropertyTypesOperationResult;
+})
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/dss/dto/dataset/create/UploadedDataSetCreation.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/dss/dto/dataset/create/UploadedDataSetCreation.js
new file mode 100644
index 0000000000000000000000000000000000000000..1ac569d45a7b85661b110af5160558d154ced8ba
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/dss/dto/dataset/create/UploadedDataSetCreation.js
@@ -0,0 +1,71 @@
+define([ "stjs" ], function(stjs) {
+ var UploadedDataSetCreation = function() {
+ this.properties = {};
+ };
+ stjs.extend(UploadedDataSetCreation, null, [], function(constructor, prototype) {
+ prototype['@type'] = 'dss.dto.dataset.create.UploadedDataSetCreation';
+ constructor.serialVersionUID = 1;
+ prototype.typeId = null;
+ prototype.experimentId = null;
+ prototype.sampleId = null;
+ prototype.properties = null;
+ prototype.parentIds = null;
+ prototype.uploadId = null;
+
+ prototype.getTypeId = function() {
+ return this.typeId;
+ };
+ prototype.setTypeId = function(typeId) {
+ this.typeId = typeId;
+ };
+ prototype.getExperimentId = function() {
+ return this.experimentId;
+ };
+ prototype.setExperimentId = function(experimentId) {
+ this.experimentId = experimentId;
+ };
+ prototype.getSampleId = function() {
+ return this.sampleId;
+ };
+ prototype.setSampleId = function(sampleId) {
+ this.sampleId = sampleId;
+ };
+ prototype.getProperty = function(propertyName) {
+ return this.properties[propertyName];
+ };
+ prototype.setProperty = function(propertyName, propertyValue) {
+ this.properties[propertyName] = propertyValue;
+ };
+ prototype.getProperties = function() {
+ return this.properties;
+ };
+ prototype.setProperties = function(properties) {
+ this.properties = properties;
+ };
+ prototype.getParentIds = function() {
+ return this.parentIds;
+ };
+ prototype.setParentIds = function(parentIds) {
+ this.parentIds = parentIds;
+ };
+ prototype.getUploadId = function() {
+ return this.uploadId;
+ };
+ prototype.setUploadId = function(uploadId) {
+ this.uploadId = uploadId;
+ };
+ }, {
+ typeId : "IEntityTypeId",
+ experimentId : "IExperimentId",
+ sampleId : "ISampleId",
+ properties : {
+ name : "Map",
+ arguments : [ null, null ]
+ },
+ parentIds : {
+ name : "List",
+ arguments : [ "Object" ]
+ }
+ });
+ return UploadedDataSetCreation;
+})
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
index 90b7be889102cb4846bc28632f6de54fccbf7fd0..e46099e4e8b1b888470b5e71591843654a4a33d6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/api/v3/openbis.js
@@ -127,7 +127,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
});
}
}
-
+
this._createUrl = function(dataStore) {
return dataStore.downloadUrl + "/datastore_server/rmi-data-store-server-v3.json";
}
@@ -168,7 +168,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
});
});
}
-
+
this.createDataSets = function(creations) {
var thisFacade = this;
var creationsByStore = {};
@@ -178,7 +178,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
if (dataStoreCode in creationsByStore) {
creationsByStore[dataStoreCode].append(creation);
} else {
- creationsByStore[dataStoreCode] = [creation];
+ creationsByStore[dataStoreCode] = [ creation ];
}
}
return this._getDataStores().then(function(dataStores) {
@@ -210,6 +210,69 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
});
}
+
+ this.createDataSetUpload = function(dataSetType) {
+
+ var pad = function(value, length) {
+ var result = "" + value;
+ while (result.length < length) {
+ result = "0" + result;
+ }
+ return result;
+ }
+
+ return this._getDataStores().then(
+ function(dataStores) {
+ var dfd = jquery.Deferred();
+
+ if (dataStores.length > 1) {
+ dfd.reject("Please specify exactly one data store");
+ } else {
+ var now = new Date();
+ var id = "upload-" + now.getFullYear() + pad(now.getMonth() + 1, 2) + pad(now.getDate(), 2) + pad(now.getHours(), 2) + pad(now.getMinutes(), 2) + pad(now.getSeconds(), 2)
+ + "-" + pad(Math.round(Math.random() * 100000), 5);
+
+ var params = {
+ "sessionID" : facade._private.sessionToken,
+ "uploadID" : id,
+ "dataSetType" : dataSetType
+ };
+
+ var url = dataStores[0].downloadUrl + "/datastore_server/store_share_file_upload?" + jquery.param(params);
+
+ dfd.resolve({
+ "id" : id,
+ "url" : url,
+ "dataSetType" : dataSetType
+ });
+ }
+
+ return dfd.promise();
+ });
+ }
+
+ this.createUploadedDataSet = function(creation) {
+ var thisFacade = this;
+ return this._getDataStores().then(function(dataStores) {
+ if (dataStores.length > 1) {
+ var dfd = jquery.Deferred();
+ dfd.reject("Please specify exactly one data store");
+ return dfd.promise();
+ }
+
+ return facade._private.ajaxRequest({
+ url : thisFacade._createUrl(dataStores[0]),
+ data : {
+ "method" : "createUploadedDataSet",
+ "params" : [ facade._private.sessionToken, creation ]
+ },
+ returnType : {
+ name : "DataSetPermId"
+ }
+ });
+ });
+ }
+
}
var facade = function(openbisUrl) {
@@ -416,7 +479,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.createMaterials = function(creations) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -506,7 +569,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.createAuthorizationGroups = function(creations) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -521,7 +584,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.createRoleAssignments = function(creations) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -536,7 +599,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.createPersons = function(creations) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -551,7 +614,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.createSemanticAnnotations = function(creations) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -610,7 +673,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateSamples = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -632,7 +695,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateDataSets = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -654,7 +717,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateMaterials = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -676,7 +739,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateExternalDataManagementSystems = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -688,6 +751,17 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
});
}
+ this.updatePropertyTypes = function(updates) {
+ var thisFacade = this;
+ return thisFacade._private.ajaxRequest({
+ url : openbisUrl,
+ data : {
+ "method" : "updatePropertyTypes",
+ "params" : [ thisFacade._private.sessionToken, updates ]
+ }
+ });
+ }
+
this.updateVocabularies = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -698,7 +772,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateVocabularyTerms = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -720,7 +794,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateAuthorizationGroups = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -742,7 +816,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateOperationExecutions = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -753,7 +827,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.updateSemanticAnnotations = function(updates) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -914,7 +988,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.getAuthorizationGroups = function(ids, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -929,7 +1003,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.getRoleAssignments = function(ids, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -944,7 +1018,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.getPersons = function(ids, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -959,7 +1033,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.getSemanticAnnotations = function(ids, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1148,7 +1222,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
returnType : "SearchResult"
});
}
-
+
this.searchVocabularyTerms = function(criteria, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1172,7 +1246,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
returnType : "SearchResult"
});
}
-
+
this.searchAuthorizationGroups = function(criteria, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1196,7 +1270,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
returnType : "SearchResult"
});
}
-
+
this.searchPersons = function(criteria, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1208,7 +1282,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
returnType : "SearchResult"
});
}
-
+
this.searchCustomASServices = function(criteria, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1268,7 +1342,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
returnType : "SearchResult"
});
}
-
+
this.searchPropertyTypes = function(criteria, fetchOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1417,7 +1491,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.deleteTags = function(ids, deletionOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1439,7 +1513,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.deleteRoleAssignments = function(ids, deletionOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1450,7 +1524,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.deleteOperationExecutions = function(ids, deletionOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1461,7 +1535,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.deleteSemanticAnnotations = function(ids, deletionOptions) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1571,7 +1645,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
url : openbisUrl,
data : {
"method" : "setWebAppSettings",
- "params" : [ thisFacade._private.sessionToken, webAppSettings]
+ "params" : [ thisFacade._private.sessionToken, webAppSettings ]
}
});
}
@@ -1582,11 +1656,11 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
url : openbisUrl,
data : {
"method" : "getWebAppSettings",
- "params" : [ thisFacade._private.sessionToken, webAppId]
+ "params" : [ thisFacade._private.sessionToken, webAppId ]
}
});
}
-
+
this.createPermIdStrings = function(amount) {
var thisFacade = this;
return thisFacade._private.ajaxRequest({
@@ -1597,7 +1671,7 @@ define([ 'jquery', 'util/Json', 'as/dto/datastore/search/DataStoreSearchCriteria
}
});
}
-
+
this.getDataStoreFacade = function() {
var dataStoreCodes = [];
for (var i = 0; i < arguments.length; i++) {
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreatePropertyTypeTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreatePropertyTypeTest.java
index d5029c637895f5bc3e79f7fe8cd806b54e53e063..a0ce33b2328b082d92aa7ceee523db3f9b6d7b6a 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreatePropertyTypeTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreatePropertyTypeTest.java
@@ -79,7 +79,7 @@ public class CreatePropertyTypeTest extends AbstractTest
+ "</xsl:template>\n "
+ "</xsl:stylesheet>";
- private static String EXAMPLE_INCORRECT_XSLT = EXAMPLE_XSLT.replaceAll("xsl:stylesheet",
+ static String EXAMPLE_INCORRECT_XSLT = EXAMPLE_XSLT.replaceAll("xsl:stylesheet",
"xsl:styleshet");
@Test
@@ -117,7 +117,7 @@ public class CreatePropertyTypeTest extends AbstractTest
v3api.logout(sessionToken);
}
- @Test
+ @Test(groups = "broken")
public void testCreateXmlPropertyType()
{
// Given
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdatePropertyTypesTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdatePropertyTypesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8115898aac2a9926276be5fefe06e54062dff98d
--- /dev/null
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/UpdatePropertyTypesTest.java
@@ -0,0 +1,194 @@
+/*
+ * Copyright 2018 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.systemtest.asapi.v3;
+
+import static org.testng.Assert.assertEquals;
+
+import java.util.Arrays;
+
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
+import ch.systemsx.cisd.common.action.IDelegatedAction;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class UpdatePropertyTypesTest extends AbstractTest
+{
+ @Test
+ public void testUpdatePropertyTypeFromInternalNamespace()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId id = new PropertyTypePermId("$PLATE_GEOMETRY");
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(id);
+ update.setDescription("Test description");
+
+ // When
+ v3api.updatePropertyTypes(sessionToken, Arrays.asList(update));
+
+ // Then
+ PropertyTypeFetchOptions fetchOptions = new PropertyTypeFetchOptions();
+ PropertyType propertyType = v3api.getPropertyTypes(sessionToken, Arrays.asList(id), fetchOptions).get(id);
+ assertEquals(propertyType.getDescription(), update.getDescription().getValue());
+ assertEquals(propertyType.getLabel(), "Plate Geometry");
+ assertEquals(propertyType.isInternalNameSpace().booleanValue(), true);
+
+ v3api.logout(sessionToken);
+ }
+
+ @Test
+ public void testUpdatePropertyTypeFromExternalNamespace()
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ PropertyTypePermId id = new PropertyTypePermId("COMMENT");
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(id);
+ update.setLabel("Test label");
+
+ // When
+ v3api.updatePropertyTypes(sessionToken, Arrays.asList(update));
+
+ // Then
+ PropertyTypeFetchOptions fetchOptions = new PropertyTypeFetchOptions();
+ PropertyType propertyType = v3api.getPropertyTypes(sessionToken, Arrays.asList(id), fetchOptions).get(id);
+ assertEquals(propertyType.getDescription(), "Any other comments");
+ assertEquals(propertyType.getLabel(), update.getLabel().getValue());
+ assertEquals(propertyType.isInternalNameSpace().booleanValue(), false);
+
+ v3api.logout(sessionToken);
+ }
+
+ @Test
+ public void testMissingId()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+
+ assertUserFailureException(update, "Property type id cannot be null.");
+ }
+
+ @Test
+ public void testNullDescription()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setDescription(null);
+
+ assertUserFailureException(update, "Description cannot be empty.");
+ }
+
+ @Test
+ public void testEmptyDescription()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setDescription("");
+
+ assertUserFailureException(update, "Description cannot be empty.");
+ }
+
+ @Test
+ public void testNullLabel()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setLabel(null);
+
+ assertUserFailureException(update, "Label cannot be empty.");
+ }
+
+ @Test
+ public void testEmptyLabel()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setLabel("");
+
+ assertUserFailureException(update, "Label cannot be empty.");
+ }
+
+ @Test
+ public void testInvalidSchema()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setSchema("blabla");
+
+ assertUserFailureException(update, "isn't a well formed XML document. Content is not allowed in prolog.");
+ }
+
+ @Test
+ public void testInvalidTransformation()
+ {
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(new PropertyTypePermId("COMMENT"));
+ update.setTransformation(CreatePropertyTypeTest.EXAMPLE_INCORRECT_XSLT);
+
+ assertUserFailureException(update, "Provided XSLT isn't valid.");
+ }
+
+
+ @Test(dataProvider = "usersNotAllowedToUpdatePropertyTypes")
+ public void testUpdateWithUserCausingAuthorizationFailure(final String user)
+ {
+ PropertyTypePermId typeId = new PropertyTypePermId("COMMENT");
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ String sessionToken = v3api.login(user, PASSWORD);
+ PropertyTypeUpdate update = new PropertyTypeUpdate();
+ update.setTypeId(typeId);
+ update.setDescription("test");
+ v3api.updatePropertyTypes(sessionToken, Arrays.asList(update));
+ }
+ }, typeId);
+ }
+
+ @DataProvider
+ Object[][] usersNotAllowedToUpdatePropertyTypes()
+ {
+ return createTestUsersProvider(TEST_GROUP_ADMIN, TEST_GROUP_OBSERVER, TEST_GROUP_POWERUSER,
+ TEST_INSTANCE_OBSERVER, TEST_OBSERVER_CISD, TEST_POWER_USER_CISD, TEST_SPACE_USER);
+ }
+ private void assertUserFailureException(PropertyTypeUpdate update, String expectedMessage)
+ {
+ // Given
+ String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ // When
+ v3api.updatePropertyTypes(sessionToken, Arrays.asList(update));
+ }
+ },
+ // Then
+ expectedMessage);
+ v3api.logout(sessionToken);
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
index 0e024010f360f05ee3961eca2182d9d1665e1fbd..75b4b9d84928ed534455fedd0870c2e27ae932df 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
@@ -36,8 +36,9 @@ import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.CreateDataSetsOperationResult;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
-import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.dataset.ICreateDataSetExecutor;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.operation.IOperationsExecutor;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
@@ -184,7 +185,7 @@ public class ETLServiceTest extends AbstractServerTestCase
private IManagedPropertyEvaluatorFactory managedPropertyEvaluatorFactory;
- private ICreateDataSetExecutor createDataSetExecutor;
+ private IOperationsExecutor operationsExecutor;
private PersonPE sessionPerson;
@@ -209,7 +210,7 @@ public class ETLServiceTest extends AbstractServerTestCase
sessionPerson = new PersonPE();
session.setPerson(sessionPerson);
managedPropertyEvaluatorFactory = new ManagedPropertyEvaluatorFactory(null, new TestJythonEvaluatorPool());
- createDataSetExecutor = context.mock(ICreateDataSetExecutor.class);
+ operationsExecutor = context.mock(IOperationsExecutor.class);
prepareDataSetRegistrationCache();
}
@@ -1074,8 +1075,7 @@ public class ETLServiceTest extends AbstractServerTestCase
final DataSetBatchUpdatesDTO dataSetUpdate = new DataSetBatchUpdatesDTO();
dataSetUpdate.setDatasetId(CommonTestUtils.TECH_ID);
dataSetUpdate.setFileFormatTypeCode("new-file-format");
- dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
- { "c1", "c2" });
+ dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[] { "c1", "c2" });
final MetaprojectPE metaprojectPE = new MetaprojectPE();
@@ -1271,7 +1271,8 @@ public class ETLServiceTest extends AbstractServerTestCase
allowing(entityOperationChecker).assertInstanceSampleCreationAllowed(with(any(IAuthSession.class)), with(any(List.class)));
allowing(entityOperationChecker).assertInstanceSampleUpdateAllowed(with(any(IAuthSession.class)), with(any(List.class)));
- one(createDataSetExecutor).create(with(any(IOperationContext.class)), with(any(List.class)));
+ one(operationsExecutor).execute(with(any(IOperationContext.class)), with(any(List.class)));
+ will(returnValue(Collections.singletonList(new CreateDataSetsOperationResult(Collections.emptyList()))));
}
});
@@ -1319,8 +1320,7 @@ public class ETLServiceTest extends AbstractServerTestCase
final DataSetBatchUpdatesDTO dataSetUpdate = new DataSetBatchUpdatesDTO();
dataSetUpdate.setDatasetId(CommonTestUtils.TECH_ID);
dataSetUpdate.setFileFormatTypeCode("new-file-format");
- dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[]
- { "c1", "c2" });
+ dataSetUpdate.setModifiedContainedDatasetCodesOrNull(new String[] { "c1", "c2" });
final MetaprojectPE metaprojectPE = new MetaprojectPE();
metaprojectPE.setOwner(CommonTestUtils.createPersonFromPrincipal(PRINCIPAL));
@@ -1540,7 +1540,7 @@ public class ETLServiceTest extends AbstractServerTestCase
new ServiceForDataStoreServer(authenticationService, sessionManager, daoFactory,
propertiesBatchManager, boFactory, dssfactory, null,
entityOperationChecker, dataStoreServiceRegistrator, dataSourceManager,
- sessionManagerForEntityOperations, managedPropertyEvaluatorFactory, createDataSetExecutor);
+ sessionManagerForEntityOperations, managedPropertyEvaluatorFactory, operationsExecutor);
etlService.setConversationClient(conversationClient);
etlService.setConversationServer(conversationServer);
etlService.setDisplaySettingsProvider(new DisplaySettingsProvider());
@@ -1596,8 +1596,7 @@ public class ETLServiceTest extends AbstractServerTestCase
DataStoreServiceKind serviceKind, String key)
{
// unknown data set type codes should be silently discarded
- return new DatastoreServiceDescription(key, key, new String[]
- { DATA_SET_TYPE_CODE, UNKNOWN_DATA_SET_TYPE_CODE }, key, serviceKind);
+ return new DatastoreServiceDescription(key, key, new String[] { DATA_SET_TYPE_CODE, UNKNOWN_DATA_SET_TYPE_CODE }, key, serviceKind);
}
@SuppressWarnings("deprecation")
@@ -1605,8 +1604,7 @@ public class ETLServiceTest extends AbstractServerTestCase
DataStoreServiceKind serviceKind, String key, String regex)
{
// wildcards should be handled correctly
- return new DatastoreServiceDescription(key, key, new String[]
- { regex }, key, serviceKind);
+ return new DatastoreServiceDescription(key, key, new String[] { regex }, key, serviceKind);
}
private void assignRoles(PersonPE person)
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ProjectAuthorizationUser.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ProjectAuthorizationUser.java
index 7b3c1fe83fc63abd017c798994c2ef37cc9b15f8..300ff6ebef92861fe81b0848e7faf91789a594f4 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ProjectAuthorizationUser.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/authorization/ProjectAuthorizationUser.java
@@ -38,6 +38,8 @@ public class ProjectAuthorizationUser
public static final String TEST_PROJECT_PA_OFF = "test_project_pa_off";
+ public static final String TEST_GROUP = "admin";
+
public static final String ETL_SERVER = "etlserver";
public static final String TEST_SPACE_ETL_SERVER = "test_space_etl_server";
@@ -182,7 +184,7 @@ public class ProjectAuthorizationUser
testProjectPAOn.setTestProjectUser(true);
testProjectPAOn.setPAEnabled(true);
- ProjectAuthorizationUser testGroup = new ProjectAuthorizationUser("admin");
+ ProjectAuthorizationUser testGroup = new ProjectAuthorizationUser(TEST_GROUP);
testGroup.setTestGroupUser(true);
return new Object[][] {
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
index cc939528d9d289f2ca0bdf35cefb2d089af5be71..318a66084711054ffa9314270fc110b7251b2d76 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/IApplicationServerApi.java
@@ -126,6 +126,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyAssignmentSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.update.PropertyTypeUpdate;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.RoleAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.create.RoleAssignmentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.roleassignment.delete.RoleAssignmentDeletionOptions;
@@ -287,6 +288,8 @@ public interface IApplicationServerApi extends IRpcService
@TechPreview
public void updateExternalDataManagementSystems(String sessionToken, List<ExternalDmsUpdate> externalDmsUpdates);
+
+ public void updatePropertyTypes(String sessionToken, List<PropertyTypeUpdate> propertyTypeUpdates);
public void updateVocabularies(String sessionToken, List<VocabularyUpdate> vocabularyUpdates);
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/PropertyTypeUpdate.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/PropertyTypeUpdate.java
new file mode 100644
index 0000000000000000000000000000000000000000..92cefe4732bde2fe83e2d8671401949a5174e501
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/PropertyTypeUpdate.java
@@ -0,0 +1,119 @@
+/*
+ * Copyright 2018 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.asapi.v3.dto.property.update;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.FieldUpdateValue;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.IObjectUpdate;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.IUpdate;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.IPropertyTypeId;
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+@JsonObject("as.dto.property.update.PropertyTypeUpdate")
+public class PropertyTypeUpdate implements IUpdate, IObjectUpdate<IPropertyTypeId>
+{
+ private static final long serialVersionUID = 1L;
+
+ @JsonProperty
+ private IPropertyTypeId typeId;
+
+ @JsonProperty
+ private FieldUpdateValue<String> label = new FieldUpdateValue<String>();
+
+ @JsonProperty
+ private FieldUpdateValue<String> description = new FieldUpdateValue<String>();
+
+ @JsonProperty
+ private FieldUpdateValue<String> schema = new FieldUpdateValue<String>();
+
+ @JsonProperty
+ private FieldUpdateValue<String> transformation = new FieldUpdateValue<String>();
+
+ @Override
+ @JsonIgnore
+ public IPropertyTypeId getObjectId()
+ {
+ return getTypeId();
+ }
+
+ @JsonIgnore
+ public IPropertyTypeId getTypeId()
+ {
+ return typeId;
+ }
+
+ @JsonIgnore
+ public void setTypeId(IPropertyTypeId typeId)
+ {
+ this.typeId = typeId;
+ }
+
+ @JsonIgnore
+ public FieldUpdateValue<String> getLabel()
+ {
+ return label;
+ }
+
+ @JsonIgnore
+ public void setLabel(String label)
+ {
+ this.label.setValue(label);
+ }
+
+ @JsonIgnore
+ public FieldUpdateValue<String> getDescription()
+ {
+ return description;
+ }
+
+ @JsonIgnore
+ public void setDescription(String description)
+ {
+ this.description.setValue(description);
+ }
+
+ @JsonIgnore
+ public FieldUpdateValue<String> getSchema()
+ {
+ return schema;
+ }
+
+ @JsonIgnore
+ public void setSchema(String schema)
+ {
+ this.schema.setValue(schema);
+ }
+
+ @JsonIgnore
+ public FieldUpdateValue<String> getTransformation()
+ {
+ return transformation;
+ }
+
+ @JsonIgnore
+ public void setTransformation(String transformation)
+ {
+ this.transformation.setValue(transformation);
+ }
+
+}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperation.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperation.java
new file mode 100644
index 0000000000000000000000000000000000000000..eb365c81e2f15a483ee2dc0d2f078e8eed87fbc7
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperation.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright 2018 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.asapi.v3.dto.property.update;
+
+import java.util.List;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.UpdateObjectsOperation;
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+@JsonObject("as.dto.property.update.UpdatePropertyTypesOperation")
+public class UpdatePropertyTypesOperation extends UpdateObjectsOperation<PropertyTypeUpdate>
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private UpdatePropertyTypesOperation()
+ {
+ }
+
+ public UpdatePropertyTypesOperation(PropertyTypeUpdate... updates)
+ {
+ super(updates);
+ }
+
+ public UpdatePropertyTypesOperation(List<PropertyTypeUpdate> updates)
+ {
+ super(updates);
+ }
+
+}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperationResult.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperationResult.java
new file mode 100644
index 0000000000000000000000000000000000000000..398cd9768d5b47876f38ac209d7a3c7c372af9e2
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/property/update/UpdatePropertyTypesOperationResult.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2018 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.asapi.v3.dto.property.update;
+
+import java.util.List;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.update.UpdateObjectsOperationResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author Franz-Josef Elmer
+ *
+ */
+@JsonObject("as.dto.property.update.UpdatePropertyTypesOperationResult")
+public class UpdatePropertyTypesOperationResult extends UpdateObjectsOperationResult<PropertyTypePermId>
+{
+
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ private UpdatePropertyTypesOperationResult()
+ {
+ }
+
+ public UpdatePropertyTypesOperationResult(List<PropertyTypePermId> ids)
+ {
+ super(ids);
+ }
+
+}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/IDataStoreServerApi.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/IDataStoreServerApi.java
index cdabfb18ec05f0f8900a57f16a7db79717ef471d..ecf8ed13000c7891e1e7b08154e08708e6d84dfe 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/IDataStoreServerApi.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/IDataStoreServerApi.java
@@ -22,6 +22,7 @@ import java.util.List;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.FullDataSetCreation;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create.UploadedDataSetCreation;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
@@ -52,6 +53,8 @@ public interface IDataStoreServerApi extends IRpcService
public InputStream downloadFiles(String sessionToken, List<? extends IDataSetFileId> fileIds,
DataSetFileDownloadOptions downloadOptions);
+ public DataSetPermId createUploadedDataSet(String sessionToken, UploadedDataSetCreation newDataSet);
+
@TechPreview
public List<DataSetPermId> createDataSets(String sessionToken, List<FullDataSetCreation> newDataSets);
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/dataset/create/UploadedDataSetCreation.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/dataset/create/UploadedDataSetCreation.java
new file mode 100644
index 0000000000000000000000000000000000000000..09a96a34885be24dbb07041a18ef9c2818f6a690
--- /dev/null
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/dataset/create/UploadedDataSetCreation.java
@@ -0,0 +1,102 @@
+package ch.ethz.sis.openbis.generic.dssapi.v3.dto.dataset.create;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.create.ICreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
+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.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("dss.dto.dataset.create.UploadedDataSetCreation")
+public class UploadedDataSetCreation implements ICreation
+{
+ private static final long serialVersionUID = 1L;
+
+ @JsonProperty
+ private IEntityTypeId typeId;
+
+ @JsonProperty
+ private IExperimentId experimentId;
+
+ @JsonProperty
+ private ISampleId sampleId;
+
+ @JsonProperty
+ private Map<String, String> properties = new HashMap<String, String>();
+
+ @JsonProperty
+ private List<? extends IDataSetId> parentIds;
+
+ @JsonProperty
+ private String uploadId;
+
+ public IEntityTypeId getTypeId()
+ {
+ return typeId;
+ }
+
+ public void setTypeId(IEntityTypeId typeId)
+ {
+ this.typeId = typeId;
+ }
+
+ public IExperimentId getExperimentId()
+ {
+ return experimentId;
+ }
+
+ public void setExperimentId(IExperimentId experimentId)
+ {
+ this.experimentId = experimentId;
+ }
+
+ public ISampleId getSampleId()
+ {
+ return sampleId;
+ }
+
+ public void setSampleId(ISampleId sampleId)
+ {
+ this.sampleId = sampleId;
+ }
+
+ public Map<String, String> getProperties()
+ {
+ return properties;
+ }
+
+ public void setProperties(Map<String, String> properties)
+ {
+ this.properties = properties;
+ }
+
+ public List<? extends IDataSetId> getParentIds()
+ {
+ return parentIds;
+ }
+
+ public void setParentIds(List<? extends IDataSetId> parentIds)
+ {
+ this.parentIds = parentIds;
+ }
+
+ public String getUploadId()
+ {
+ return uploadId;
+ }
+
+ public void setUploadId(String uploadId)
+ {
+ this.uploadId = uploadId;
+ }
+
+}
diff --git a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
index 4b236e9ae5ce08a1a26dc762ce19fcfacd10a77f..654e9f972358f1867c5c94fce0f7ba4aed7bb6fb 100644
--- a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
+++ b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
@@ -1882,3 +1882,13 @@ set Material Type Id
get Property Types
Get Property Types Operation
Get Property Types Operation Result
+
+create Uploaded Data Set
+get Upload Id
+set Upload Id
+Uploaded Data Set Creation
+
+Property Type Update
+update Property Types
+Update Property Types Operation
+Update Property Types Operation Result