diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..302b053695844f404be0ccc66d9213d1b5ab4111
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/FacadeFactory.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
+
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.openbis.generic.shared.DefaultLimsServiceStubFactory;
+import ch.systemsx.cisd.openbis.generic.shared.OpenBisServiceFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.Constants;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+
+/**
+ * Factory of {@link IRawDataApiFacade}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FacadeFactory
+{
+ private static final int SERVER_TIMEOUT_MIN = 5;
+
+ // Trick for discovering the server Url
+ private static String getServiceUrl(String serverUrl)
+ {
+ OpenBisServiceFactory openBisServiceFactory =
+ new OpenBisServiceFactory(serverUrl, new DefaultLimsServiceStubFactory());
+ openBisServiceFactory.createService();
+ return openBisServiceFactory.getUsedServerUrl() + Constants.RAW_DATA_SERVER_URL;
+ }
+
+ /**
+ * Creates a facade for specified server URL, user Id, and password.
+ */
+ public static IRawDataApiFacade create(String serverURL, String userID, String password)
+ {
+ String serviceUrl = getServiceUrl(serverURL);
+ IRawDataService service =
+ HttpInvokerUtils.createServiceStub(IRawDataService.class, serviceUrl,
+ SERVER_TIMEOUT_MIN);
+ String sessionToken = service.tryToAuthenticateAtRawDataServer(userID, password);
+ if (sessionToken == null)
+ {
+ throw new IllegalArgumentException("User " + userID + " couldn't be authenticated");
+ }
+ return new RawDataApiFacade(service, sessionToken);
+ }
+
+ /**
+ * Creates a facade for specified url and sessionToken.
+ */
+ public static IRawDataApiFacade create(String serverURL, String sessionToken)
+ {
+ IRawDataService service =
+ HttpInvokerUtils.createServiceStub(IRawDataService.class, serverURL
+ + Constants.RAW_DATA_SERVER_URL, SERVER_TIMEOUT_MIN);
+ return new RawDataApiFacade(service, sessionToken);
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
new file mode 100644
index 0000000000000000000000000000000000000000..99d733148d488908528c6318d91073193b4a5b3a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
+
+
+/**
+ * Facade for openBIS PhosphoNetX raw data (aka MS_INJECTION data) service.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IRawDataApiFacade
+{
+ /**
+ * Return the session token for the logged-in user.
+ */
+ public String getSessionToken();
+
+ /**
+ * Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which
+ * the specified user is allow to read.
+ */
+ public List<MsInjectionDataInfo> listRawDataSamples(String userID);
+
+ /**
+ * Lists all processing plugins on DSS.
+ */
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos();
+
+ /**
+ * Processes the data sets of specified samples by the DSS processing plug-in of specified key
+ * for the specified user.
+ */
+ public void processingRawData(String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs, String dataSetType);
+
+ /**
+ * Logs current user out.
+ */
+ public void logout();
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java
new file mode 100644
index 0000000000000000000000000000000000000000..4ef94ccef81c294c87d02647cfb501c2525d425c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiFacade.java
@@ -0,0 +1,68 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class RawDataApiFacade implements IRawDataApiFacade
+{
+ private final IRawDataService service;
+ private final String sessionToken;
+
+ RawDataApiFacade(IRawDataService service, String sessionToken)
+ {
+ this.service = service;
+ this.sessionToken = sessionToken;
+ }
+
+ public String getSessionToken()
+ {
+ return sessionToken;
+ }
+
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos()
+ {
+ return service.listDataStoreServerProcessingPluginInfos(sessionToken);
+ }
+
+ public List<MsInjectionDataInfo> listRawDataSamples(String userID)
+ {
+ return service.listRawDataSamples(sessionToken, userID);
+ }
+
+ public void processingRawData(String userID, String dataSetProcessingKey,
+ long[] rawDataSampleIDs, String dataSetType)
+ {
+ service.processingRawData(sessionToken, userID, dataSetProcessingKey, rawDataSampleIDs,
+ dataSetType);
+ }
+
+ public void logout()
+ {
+ service.logout(sessionToken);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c456ae7f8fbde16781291840c61c477b80ef38d9
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/RawDataApiTest.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
+
+import java.util.Date;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class RawDataApiTest
+{
+ public static void main(String[] args)
+ {
+ if (args.length != 4)
+ {
+ System.err.println("Usage: <openbis-server-url> <login id> <password> <user id>");
+ return;
+ }
+
+ String serverURL = args[0];
+ String loginID = args[1];
+ String password = args[2];
+ String userID = args[3];
+ IRawDataApiFacade facade = FacadeFactory.create(serverURL, loginID, password);
+
+ System.out.println("MS_INJECTION samples:");
+ List<MsInjectionDataInfo> rawDataSamples = facade.listRawDataSamples(userID);
+ for (MsInjectionDataInfo info : rawDataSamples)
+ {
+ Map<String, Date> latestDataSets = info.getLatestDataSetRegistrationDates();
+ if (latestDataSets.isEmpty() == false)
+ {
+ System.out.println(" " + info.getMsInjectionSampleCode() + " -> "
+ + info.getBiologicalSampleIdentifier() + ": latest data sets: "
+ + latestDataSets);
+ }
+ }
+
+ System.out.println("DSS processing plugins:");
+ List<DataStoreServerProcessingPluginInfo> infos = facade.listDataStoreServerProcessingPluginInfos();
+ for (DataStoreServerProcessingPluginInfo info : infos)
+ {
+ System.out.println(" key:" + info.getKey() + ", label:'" + info.getLabel()
+ + "', data set types:" + info.getDatasetTypeCodes());
+ }
+ facade.logout();
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index 5281e1fe0ab9529d0b3135303b0fb3531d87a0ea..af71ac31a8d92c517a07d7ebb4caa671923924b3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListPro
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
index 67129c0951447efad73a2ff5f5f902dd253d0df0..f8a58957e7f53853d8a5e3ac7a0f7fd9fe981ee1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProvider.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..afc228880b9ed429f14ee1de82855086abbad536
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/Constants.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Constants
+{
+ public final static String RAW_DATA_SERVER_URL = "/rmi-phosphonetx-raw-data-v1";
+ public final static String PHOSPHONETX_RAW_DATA_SERVICE = "phosphonetx-raw-data-service";
+ public final static String PHOSPHONETX_RAW_DATA_SERVICE_INTERNAL = "phosphonetx-raw-data-service-internal";
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java
index 474519b9b20c9c81a89eb9fa1e59d6ce0d884af5..43f833667514668d70c7ea55538ba27d570fe2f5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataService.java
@@ -16,9 +16,18 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1;
+import java.io.Serializable;
import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Set;
+import java.util.Map.Entry;
+
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Component;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -26,24 +35,33 @@ import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
-import ch.systemsx.cisd.openbis.generic.shared.translator.DataStoreServiceTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.util.DataTypeUtils;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.PropertyKey;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
- * Imlementation of {@link IRawDataService}.
+ * Implementation of {@link IRawDataService}.
*
* @author Franz-Josef Elmer
*/
+@Component(Constants.PHOSPHONETX_RAW_DATA_SERVICE)
public class RawDataService extends AbstractServer<IRawDataService> implements IRawDataService
{
+ @Resource(name = Constants.PHOSPHONETX_RAW_DATA_SERVICE_INTERNAL)
private IRawDataServiceInternal service;
public RawDataService()
@@ -57,22 +75,28 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
this.service = service;
}
+ public String tryToAuthenticateAtRawDataServer(String userID, String userPassword)
+ {
+ SessionContextDTO session = tryToAuthenticate(userID, userPassword);
+ return session == null ? null : session.getSessionToken();
+ }
+
public IRawDataService createLogger(IInvocationLoggerContext context)
{
return new RawDataServiceLogger(getSessionManager(), context);
}
- public List<Sample> listRawDataSamples(String sessionToken, String userID)
+ public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
List<MsInjectionSample> list = service.listRawDataSamples(session.getSessionToken());
- ArrayList<Sample> result = new ArrayList<Sample>();
+ ArrayList<MsInjectionDataInfo> result = new ArrayList<MsInjectionDataInfo>();
for (MsInjectionSample sample : list)
{
- result.add(sample.getSample());
+ result.add(translate(sample));
}
return result;
@@ -82,11 +106,46 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
}
}
- public List<DatastoreServiceDescription> listDataStoreServices(String sessionToken)
+ private MsInjectionDataInfo translate(MsInjectionSample sample)
+ {
+ MsInjectionDataInfo info = new MsInjectionDataInfo();
+ Sample msiSample = sample.getSample();
+ info.setMsInjectionSampleID(msiSample.getId());
+ info.setMsInjectionSampleCode(msiSample.getCode());
+ info.setMsInjectionSampleRegistrationDate(msiSample.getRegistrationDate());
+ info.setMsInjectionSampleProperties(translate(msiSample.getProperties()));
+ Sample bioSample = msiSample.getGeneratedFrom();
+ info.setBiologicalSampleID(bioSample.getId());
+ info.setBiologicalSampleIdentifier(bioSample.getIdentifier());
+ info.setBiologicalSampleProperties(translate(bioSample.getProperties()));
+ Map<String, Date> latestDataSetRegistrationDates = new HashMap<String, Date>();
+ for (Entry<String, ExternalData> entry : sample.getLatestDataSets().entrySet())
+ {
+ latestDataSetRegistrationDates.put(entry.getKey(), entry.getValue().getRegistrationDate());
+ }
+ info.setLatestDataSetRegistrationDates(latestDataSetRegistrationDates);
+ return info;
+ }
+
+ private Map<PropertyKey, Serializable> translate(List<IEntityProperty> properties)
+ {
+ HashMap<PropertyKey, Serializable> map = new HashMap<PropertyKey, Serializable>();
+ for (IEntityProperty property : properties)
+ {
+ PropertyType propertyType = property.getPropertyType();
+ PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
+ DataTypeCode dataTypeCode = propertyType.getDataType().getCode();
+ map.put(key, DataTypeUtils.convertValueTo(dataTypeCode, property.tryGetAsString()));
+ }
+ return map;
+ }
+
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
+ String sessionToken)
{
checkSession(sessionToken);
- List<DatastoreServiceDescription> result = new ArrayList<DatastoreServiceDescription>();
+ List<DataStoreServerProcessingPluginInfo> result = new ArrayList<DataStoreServerProcessingPluginInfo>();
List<DataStorePE> dataStores = getDAOFactory().getDataStoreDAO().listDataStores();
for (DataStorePE dataStore : dataStores)
{
@@ -95,22 +154,35 @@ public class RawDataService extends AbstractServer<IRawDataService> implements I
{
if (dataStoreService.getKind() == DataStoreServiceKind.PROCESSING)
{
- result.add(DataStoreServiceTranslator.translate(dataStoreService));
+ result.add(translate(dataStoreService));
}
}
}
return result;
}
+ private DataStoreServerProcessingPluginInfo translate(DataStoreServicePE dataStoreService)
+ {
+ String key = dataStoreService.getKey();
+ String label = dataStoreService.getLabel();
+ List<String> translatedCodes = new ArrayList<String>();
+ Set<DataSetTypePE> datasetTypes = dataStoreService.getDatasetTypes();
+ for (DataSetTypePE dataSetType : datasetTypes)
+ {
+ translatedCodes.add(dataSetType.getCode());
+ }
+ return new DataStoreServerProcessingPluginInfo(key, label, translatedCodes);
+ }
+
public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs)
+ long[] rawDataSampleIDs, String dataSetType)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
service.processRawData(session.getSessionToken(), dataSetProcessingKey,
- rawDataSampleIDs, "");
+ rawDataSampleIDs, dataSetType);
} finally
{
service.logout(session.getSessionToken());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternal.java
index 48d4b7a0f97bdf9943fba1e40e73f13204ca8e88..765b45f16c738d58eb9f442d9e796b3123ebd60e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternal.java
@@ -45,7 +45,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.Manager;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalLogger.java
index 23357a0e7e19c453679d3f69798a785c465a5ced..047e933592d2b359448732e252271786b915c4f9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalLogger.java
@@ -22,7 +22,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java
index 6674e8ebf007ea31a1dfd73af3e740c846b88bcd..98cf6922d7a460b95ae88081f3fcc9c5480cf132 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceLogger.java
@@ -21,10 +21,10 @@ import java.util.List;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
/**
* @author Franz-Josef Elmer
@@ -37,25 +37,31 @@ class RawDataServiceLogger extends AbstractServerLogger implements IRawDataServi
super(sessionManager, context);
}
- public List<Sample> listRawDataSamples(String sessionToken, String userID)
+ public String tryToAuthenticateAtRawDataServer(String userID, String userPassword)
+ {
+ return null;
+ }
+
+ public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID)
{
logAccess(sessionToken, "list_raw_data_samples", "USER_ID(%s)", userID);
return null;
}
- public List<DatastoreServiceDescription> listDataStoreServices(String sessionToken)
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
+ String sessionToken)
{
logAccess(sessionToken, "list_data_store_services", "");
return null;
}
public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs)
+ long[] rawDataSampleIDs, String dataSetType)
{
int numberOfDataSets = rawDataSampleIDs == null ? 0 : rawDataSampleIDs.length;
logAccess(sessionToken, "copy_raw_data",
- "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s)", userID,
- dataSetProcessingKey, numberOfDataSets);
+ "USER_ID(%s) DSS_PROCESSING_PLUGIN(%s) NUMBER_OF_DATA_SETS(%s) DATA_SET_TYPE(%s)",
+ userID, dataSetProcessingKey, numberOfDataSets, dataSetType);
}
public int getMajorVersion()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java
index a0a2d29992bf478a7065ef73a7a0e531ffc39806..d3a1eb303e91612fdb09e892278a70723874324d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceServer.java
@@ -25,7 +25,7 @@ import org.springframework.web.bind.annotation.RequestMapping;
import ch.systemsx.cisd.common.api.IRpcServiceNameServer;
import ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO;
import ch.systemsx.cisd.common.api.server.RpcServiceNameServer;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+import ch.systemsx.cisd.common.spring.ServiceExceptionTranslator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
/**
@@ -35,10 +35,10 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService
*/
@Controller
@RequestMapping(
- { "/rmi-phosphonetx-raw-data-v1", "/openbis/rmi-phosphonetx-raw-data-v1" })
+ { Constants.RAW_DATA_SERVER_URL, "/openbis" + Constants.RAW_DATA_SERVER_URL })
public class RawDataServiceServer extends HttpInvokerServiceExporter
{
- @Resource(name = ResourceNames.PHOSPHONETX_RAW_DATA_SERVICE)
+ @Resource(name = Constants.PHOSPHONETX_RAW_DATA_SERVICE)
private IRawDataService service;
@Resource(name = IRpcServiceNameServer.PREFFERED_BEAN_NAME)
@@ -49,9 +49,11 @@ public class RawDataServiceServer extends HttpInvokerServiceExporter
{
setServiceInterface(IRawDataService.class);
setService(service);
+ setInterceptors(new Object[]
+ { new ServiceExceptionTranslator() });
RpcServiceInterfaceVersionDTO ifaceVersion =
new RpcServiceInterfaceVersionDTO("phosphonetx-raw-data",
- "/rmi-phosphonetx-raw-data-v1", 1, 0);
+ Constants.RAW_DATA_SERVER_URL, 1, 0);
nameServer.addSupportedInterfaceVersion(ifaceVersion);
super.afterPropertiesSet();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
similarity index 96%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataServiceInternal.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
index e530b3934520522b122acca60ab3afac5850a214..72c86d06156111acd5c0ebfe19bc4a772710722b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IRawDataServiceInternal.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared;
import java.util.List;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
index a0c44142b195e0f13b1728e6ff0118579a8f09c5..f33481e74974a58eb523fb89bbe2cb12dd0db3f2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/ResourceNames.java
@@ -31,8 +31,6 @@ public class ResourceNames
public final static String PHOSPHONETX_PLUGIN_SERVER = "phosphonetx-plugin-server";
- public final static String PHOSPHONETX_RAW_DATA_SERVICE = "phosphonetx-raw-data-service";
-
public final static String PHOSPHONETX_RAW_DATA_SERVICE_WEB = "phosphonetx-raw-data-service-web";
public final static String PHOSPHONETX_DAO_FACTORY = "phosphonetx-dao-factory";
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java
index 62660fca22e7008aba6713302a63359504d1c12f..133dad42279b9d58c1c3985377a33033b0bfc9a2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IRawDataService.java
@@ -21,34 +21,48 @@ import java.util.List;
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
-import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
/**
* Service for querying raw data.
*
* @author Franz-Josef Elmer
*/
-public interface IRawDataService extends IServer, IRpcService
+public interface IRawDataService extends IRpcService
{
+ /**
+ * Tries to authenticate specified user with specified password. Returns session token if
+ * succeeded otherwise <code>null</code> is returned.
+ */
+ @Transactional
+ // this is not a readOnly transaction - it can create new users
+ public String tryToAuthenticateAtRawDataServer(String userID, String userPassword);
+
+ /**
+ * Logout the session with the specified session token.
+ */
+ @Transactional(readOnly = true)
+ public void logout(String sessionToken);
+
/**
* Returns all samples of type MS_INJECTION in space MS_DATA which have a parent sample which
* the specified user is allow to read.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
- public List<Sample> listRawDataSamples(String sessionToken, String userID);
+ public List<MsInjectionDataInfo> listRawDataSamples(String sessionToken, String userID);
/**
- * Lists all processing DSS services.
+ * Lists all processing plugins on DSS.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
- public List<DatastoreServiceDescription> listDataStoreServices(String sessionToken);
-
+ public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
+ String sessionToken);
+
/**
* Processes the data sets of specified samples by the DSS processing plug-in of specified key
* for the specified user. Implementations should check that the specified user is allowed to
@@ -57,5 +71,5 @@ public interface IRawDataService extends IServer, IRpcService
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.INSTANCE_ADMIN_OBSERVER)
public void processingRawData(String sessionToken, String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs);
+ long[] rawDataSampleIDs, String dataSetType);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..efac990c0182800fd028118243310e8b7d407191
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataStoreServerProcessingPluginInfo.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Information about a processing plugin on a Data Store Server (DSS).
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStoreServerProcessingPluginInfo implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+ private final String key;
+ private final String label;
+ private final List<String> datasetTypeCodes;
+
+ /**
+ * Create a new instance for specified key, label and data set type codes.
+ */
+ public DataStoreServerProcessingPluginInfo(String key, String label, List<String> datasetTypeCodes)
+ {
+ this.key = key;
+ this.label = label;
+ this.datasetTypeCodes = Collections.unmodifiableList(new ArrayList<String>(datasetTypeCodes));
+ }
+
+ /**
+ * Returns a unique key of the plugin.
+ */
+ public String getKey()
+ {
+ return key;
+ }
+
+ /**
+ * Returns a human readable name of the plugin.
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * Returns a list data set type codes for all data sets for which the plugin is available.
+ */
+ public List<String> getDatasetTypeCodes()
+ {
+ return datasetTypeCodes;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..912c6f56ace6833f798287cf8c865f2daff11f17
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java
@@ -0,0 +1,128 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.Map;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class MsInjectionDataInfo implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private long msInjectionSampleID;
+
+ private String msInjectionSampleCode;
+
+ private Date msInjectionSampleRegistrationDate;
+
+ private Map<PropertyKey, Serializable> msInjectionSampleProperties;
+
+ private long biologicalSampleID;
+
+ private String biologicalSampleIdentifier;
+
+ private Map<PropertyKey, Serializable> biologicalSampleProperties;
+
+ private Map<String, Date> latestDataSetRegistrationDates;
+
+ public long getMsInjectionSampleID()
+ {
+ return msInjectionSampleID;
+ }
+
+ public void setMsInjectionSampleID(long msInjectionSampleID)
+ {
+ this.msInjectionSampleID = msInjectionSampleID;
+ }
+
+ public String getMsInjectionSampleCode()
+ {
+ return msInjectionSampleCode;
+ }
+
+ public void setMsInjectionSampleCode(String msInjectionSampleCode)
+ {
+ this.msInjectionSampleCode = msInjectionSampleCode;
+ }
+
+ public Date getMsInjectionSampleRegistrationDate()
+ {
+ return msInjectionSampleRegistrationDate;
+ }
+
+ public void setMsInjectionSampleRegistrationDate(Date msInjectionSampleRegistrationDate)
+ {
+ this.msInjectionSampleRegistrationDate = msInjectionSampleRegistrationDate;
+ }
+
+ public Map<PropertyKey, Serializable> getMsInjectionSampleProperties()
+ {
+ return msInjectionSampleProperties;
+ }
+
+ public void setMsInjectionSampleProperties(
+ Map<PropertyKey, Serializable> msInjectionSampleProperties)
+ {
+ this.msInjectionSampleProperties = msInjectionSampleProperties;
+ }
+
+ public long getBiologicalSampleID()
+ {
+ return biologicalSampleID;
+ }
+
+ public void setBiologicalSampleID(long biologicalSampleID)
+ {
+ this.biologicalSampleID = biologicalSampleID;
+ }
+
+ public String getBiologicalSampleIdentifier()
+ {
+ return biologicalSampleIdentifier;
+ }
+
+ public void setBiologicalSampleIdentifier(String biologicalSampleIdentifier)
+ {
+ this.biologicalSampleIdentifier = biologicalSampleIdentifier;
+ }
+
+ public Map<PropertyKey, Serializable> getBiologicalSampleProperties()
+ {
+ return biologicalSampleProperties;
+ }
+
+ public void setBiologicalSampleProperties(Map<PropertyKey, Serializable> biologicalSampleProperties)
+ {
+ this.biologicalSampleProperties = biologicalSampleProperties;
+ }
+
+ public Map<String, Date> getLatestDataSetRegistrationDates()
+ {
+ return latestDataSetRegistrationDates;
+ }
+
+ public void setLatestDataSetRegistrationDates(Map<String, Date> latestDataSetRegistrationDates)
+ {
+ this.latestDataSetRegistrationDates = latestDataSetRegistrationDates;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/PropertyKey.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/PropertyKey.java
new file mode 100644
index 0000000000000000000000000000000000000000..55ead925fe56ab16d86567be4f515ee39c20cbb4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/PropertyKey.java
@@ -0,0 +1,90 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+/**
+ * Immutable class of a property key. Two instances are equal if their IDs are equal.
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class PropertyKey implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private final String id;
+
+ private final String label;
+
+ /**
+ * Creates a new instance for specified ID and label.
+ */
+ public PropertyKey(String id, String label)
+ {
+ this.id = id;
+ this.label = label;
+ }
+
+ /**
+ * Returns the ID.
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Returns the label.
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj instanceof PropertyKey == false)
+ {
+ return false;
+ }
+ PropertyKey key = (PropertyKey) obj;
+ return key.id.equals(id);
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return id.hashCode();
+ }
+
+ /**
+ * Renders this key in the form <code><label>[<id>]</code>.
+ */
+ @Override
+ public String toString()
+ {
+ return label + "[" + id + "]";
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index a466d08b7d928da47426e165122623dd60f0db4a..e79a58284e8cb7b2d4031401a11063571719a024 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -44,7 +44,7 @@
// Raw Data Server
-->
- <bean id="phosphonetx-raw-data-service" class="org.springframework.aop.framework.ProxyFactoryBean">
+ <!--bean id="phosphonetx-raw-data-service" class="org.springframework.aop.framework.ProxyFactoryBean">
<property name="proxyInterfaces">
<list>
<value>ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService</value>
@@ -62,7 +62,7 @@
<value>exception-translator</value>
</list>
</property>
- </bean>
+ </bean-->
<bean id="phosphonetx-raw-data-service-internal"
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.RawDataServiceInternal"
diff --git a/rtd_phosphonetx/source/java/service.properties b/rtd_phosphonetx/source/java/service.properties
index 6881016234e9f4ea7ddd1d51d295a0d3da33d6dd..27d336408e81a1b2fbe783040c21bc9b17be110f 100644
--- a/rtd_phosphonetx/source/java/service.properties
+++ b/rtd_phosphonetx/source/java/service.properties
@@ -62,7 +62,17 @@ hibernate.search.index-mode = SKIP_IF_MARKER_FOUND
hibernate.search.batch-size = 1000
-query-database.label = Protein Data
-query-database.databaseEngineCode = ${phosphonetx.database.engine}
-query-database.basicDatabaseName = phosphonetx
-query-database.databaseKind = ${phosphonetx.database.kind}
+# Database Configurations for Query module
+query-databases = 1, 2
+
+1.label = openBIS meta data
+#1.data-space = CISD
+#1.creator-minimal-role = SPACE_ADMIN
+1.database-driver = org.postgresql.Driver
+1.database-url = jdbc:postgresql://localhost/openbis_${database.kind}
+#1.database-username =
+#1.database-pasword =
+
+2.label = Protein Data
+2.database-driver = org.postgresql.Driver
+2.database-url = jdbc:postgresql://localhost/phosphonetx_${phosphonetx.database.kind}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
index f3e89ccbc7a0ea95989374f861338c514a1a298a..c3691ffd914f662d059062f13a6804c21000fe13 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/RawDataTestClient.java
@@ -22,10 +22,9 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.generic.shared.DefaultLimsServiceStubFactory;
import ch.systemsx.cisd.openbis.generic.shared.OpenBisServiceFactory;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
/**
* @author Franz-Josef Elmer
@@ -57,20 +56,19 @@ public class RawDataTestClient
try
{
System.out.println("User: " + user);
- SessionContextDTO session = service.tryToAuthenticate("test", "a");
- String sessionToken = session.getSessionToken();
- List<DatastoreServiceDescription> services =
- service.listDataStoreServices(sessionToken);
- for (DatastoreServiceDescription datastoreServiceDescription : services)
+ String sessionToken = service.tryToAuthenticateAtRawDataServer("test", "a");
+ List<DataStoreServerProcessingPluginInfo> services =
+ service.listDataStoreServerProcessingPluginInfos(sessionToken);
+ for (DataStoreServerProcessingPluginInfo info : services)
{
- System.out.print(datastoreServiceDescription.getLabel() + " ");
+ System.out.print(info.getLabel() + " ");
}
System.out.println();
- List<Sample> samples = service.listRawDataSamples(sessionToken, user);
- for (Sample sample : samples)
+ List<MsInjectionDataInfo> samples = service.listRawDataSamples(sessionToken, user);
+ for (MsInjectionDataInfo sample : samples)
{
- System.out.println(" " + sample.getCode() + " -> "
- + sample.getGeneratedFrom().getIdentifier());
+ System.out.println(" " + sample.getMsInjectionSampleCode() + " -> "
+ + sample.getBiologicalSampleIdentifier());
}
} catch (UserFailureException ex)
{
@@ -79,16 +77,15 @@ public class RawDataTestClient
}
System.out.println("--------------------");
- SessionContextDTO session = service.tryToAuthenticate("test_b", "t");
- String sessionToken = session.getSessionToken();
+ String sessionToken = service.tryToAuthenticateAtRawDataServer("test_b", "t");
- List<Sample> samples = service.listRawDataSamples(sessionToken, "test_a");
+ List<MsInjectionDataInfo> samples = service.listRawDataSamples(sessionToken, "test_a");
long[] ids = new long[samples.size()];
for (int i = 0; i < samples.size(); i++)
{
- Sample sample = samples.get(i);
- ids[i] = sample.getId();
+ MsInjectionDataInfo sample = samples.get(i);
+ ids[i] = sample.getMsInjectionSampleID();
}
- service.processingRawData(sessionToken, "test_a", "copy-data-sets", ids);
+ service.processingRawData(sessionToken, "test_a", "copy-data-sets", ids, null);
}
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
index cca65ff5a600f0cd514307eb422fa8c281a70782..816d9e7278cc963fc445162ba49a6bba5489c9d1 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityPrope
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
index 9b67cfc1fe815a2d39d4b34f1e69c2470ddeae5c..c80fdc3802b560e6eb2d7e6553e1780de287f692 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceTest.java
@@ -16,8 +16,13 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
+import java.io.Serializable;
import java.util.Arrays;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
@@ -25,11 +30,25 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.RawDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataService;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.PropertyKey;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**
@@ -39,6 +58,9 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*/
public class RawDataServiceTest extends AbstractServerTestCase
{
+ private static final String RAW_DATA = "RAW_DATA";
+ private static final String MZXML_DATA = "MZXML_DATA";
+
private IRawDataServiceInternal internalService;
private IRawDataService service;
private SessionContextDTO session2;
@@ -54,12 +76,45 @@ public class RawDataServiceTest extends AbstractServerTestCase
session2.setSessionToken(SESSION_TOKEN + "2");
}
+ @Test
+ public void testListDataStoreServerProcessingPluginInfos()
+ {
+ prepareGetSession();
+ DataStoreServicePE s1 = new DataStoreServicePE();
+ s1.setKind(DataStoreServiceKind.QUERIES);
+ DataStoreServicePE s2 = new DataStoreServicePE();
+ s2.setKind(DataStoreServiceKind.PROCESSING);
+ s2.setKey("my-key");
+ s2.setLabel("my label");
+ DataSetTypePE dataSetType = new DataSetTypePE();
+ dataSetType.setCode("my type");
+ s2.setDatasetTypes(Collections.singleton(dataSetType));
+ final DataStorePE store = new DataStorePE();
+ store.setServices(new HashSet<DataStoreServicePE>(Arrays.asList(s1, s2)));
+ context.checking(new Expectations()
+ {
+ {
+ one(dataStoreDAO).listDataStores();
+ will(returnValue(Arrays.asList(store)));
+ }
+ });
+
+ List<DataStoreServerProcessingPluginInfo> infos =
+ service.listDataStoreServerProcessingPluginInfos(SESSION_TOKEN);
+
+ assertEquals(s2.getKey(), infos.get(0).getKey());
+ assertEquals(s2.getLabel(), infos.get(0).getLabel());
+ assertEquals(Arrays.asList(dataSetType.getCode()), infos.get(0).getDatasetTypeCodes());
+ assertEquals(1, infos.size());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testListRawDataSamplesForUnknownUser()
{
prepareGetSession();
prepareLoginLogout(null);
-
+
try
{
service.listRawDataSamples(SESSION_TOKEN, "abc");
@@ -78,18 +133,48 @@ public class RawDataServiceTest extends AbstractServerTestCase
prepareGetSession();
prepareLoginLogout(session2);
final Sample sample = new Sample();
+ sample.setId(4711L);
+ sample.setCode("ms-inj-42");
+ sample.setRegistrationDate(new Date(4711));
+ IEntityProperty p1 = property("integer", DataTypeCode.INTEGER, "123456");
+ IEntityProperty p2 = property("real", DataTypeCode.REAL, "1.25");
+ IEntityProperty p3 = property("string", DataTypeCode.VARCHAR, "hello");
+ sample.setProperties(Arrays.asList(p1, p2, p3));
+ Sample parent = new Sample();
+ parent.setId(4710L);
+ parent.setIdentifier("parent");
+ IEntityProperty p4 = property("boolean", DataTypeCode.BOOLEAN, "true");
+ IEntityProperty p5 = property("link", DataTypeCode.HYPERLINK, "link");
+ parent.setProperties(Arrays.asList(p4, p5));
+ sample .setGeneratedFrom(parent);
context.checking(new Expectations()
{
{
one(internalService).listRawDataSamples(session2.getSessionToken());
- will(returnValue(Arrays.asList(new MsInjectionSample(sample))));
+ MsInjectionSample msInjectionSample = new MsInjectionSample(sample);
+ msInjectionSample.addLatestDataSet(createDataSet(RAW_DATA, 10));
+ msInjectionSample.addLatestDataSet(createDataSet(MZXML_DATA, 20));
+ msInjectionSample.addLatestDataSet(createDataSet(MZXML_DATA, 15));
+ msInjectionSample.addLatestDataSet(createDataSet(RAW_DATA, 30));
+ will(returnValue(Arrays.asList(msInjectionSample)));
}
});
- List<Sample> samples = service.listRawDataSamples(SESSION_TOKEN, "abc");
+ List<MsInjectionDataInfo> infos = service.listRawDataSamples(SESSION_TOKEN, "abc");
- assertSame(sample, samples.get(0));
- assertEquals(1, samples.size());
+ MsInjectionDataInfo info = infos.get(0);
+ assertEquals(sample.getId().longValue(), info.getMsInjectionSampleID());
+ assertEquals(sample.getCode(), info.getMsInjectionSampleCode());
+ assertEquals(sample.getRegistrationDate(), info.getMsInjectionSampleRegistrationDate());
+ checkProperties(info.getMsInjectionSampleProperties(), p1, p2, p3);
+ assertEquals(parent.getId().longValue(), info.getBiologicalSampleID());
+ assertEquals(parent.getIdentifier(), info.getBiologicalSampleIdentifier());
+ checkProperties(info.getBiologicalSampleProperties(), p4, p5);
+ Map<String, Date> dates = info.getLatestDataSetRegistrationDates();
+ assertEquals(30, dates.get(RAW_DATA).getTime());
+ assertEquals(20, dates.get(MZXML_DATA).getTime());
+ assertEquals(2, dates.size());
+ assertEquals(1, infos.size());
context.assertIsSatisfied();
}
@@ -101,7 +186,7 @@ public class RawDataServiceTest extends AbstractServerTestCase
try
{
- service.processingRawData(SESSION_TOKEN, "abc", null, new long[0]);
+ service.processingRawData(SESSION_TOKEN, "abc", null, new long[0], null);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
@@ -120,11 +205,11 @@ public class RawDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).processRawData(session2.getSessionToken(), null, ids, "");
+ one(internalService).processRawData(session2.getSessionToken(), null, ids, "my-type");
}
});
- service.processingRawData(SESSION_TOKEN, "abc", null, ids);
+ service.processingRawData(SESSION_TOKEN, "abc", null, ids, "my-type");
context.assertIsSatisfied();
}
@@ -144,5 +229,38 @@ public class RawDataServiceTest extends AbstractServerTestCase
}
});
}
+
+ private void checkProperties(Map<PropertyKey, Serializable> properties, IEntityProperty... expectedProperties)
+ {
+ for (IEntityProperty expectedProperty : expectedProperties)
+ {
+ PropertyType propertyType = expectedProperty.getPropertyType();
+ PropertyKey key = new PropertyKey(propertyType.getCode(), propertyType.getLabel());
+ Serializable v = properties.get(key);
+ assertNotNull("Missing property: " + key, v);
+ assertEquals("Property " + propertyType, expectedProperty.tryGetAsString(), String.valueOf(v));
+ }
+ assertEquals(expectedProperties.length, properties.size());
+ }
+ private IEntityProperty property(String code, DataTypeCode dataTypeCode, String value)
+ {
+ EntityProperty property = new EntityProperty();
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(code.toUpperCase());
+ propertyType.setLabel(code);
+ propertyType.setDataType(new DataType(dataTypeCode));
+ property.setPropertyType(propertyType);
+ property.setValue(value);
+ return property;
+ }
+
+ private ExternalData createDataSet(String type, long date)
+ {
+ ExternalData dataSet = new ExternalData();
+ dataSet.setDataSetType(new DataSetType(type));
+ dataSet.setRegistrationDate(new Date(date));
+ return dataSet;
+ }
+
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalTest.java
index 492c65e3c2c17c67774b5f821a127728c8ca9138..989db34be68f6695e7c7b96589393665c44a52f9 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/RawDataServiceInternalTest.java
@@ -51,7 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.api.v1.RawDataServiceInternal;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IRawDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IRawDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
/**