diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
index c3317ebb5bd45aab723cc78ce97671bc6cfc216d..ab0a2a73cb5646896ef5072e31b36b7982dab4d2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IProteomicsDataApiFacade.java
@@ -80,7 +80,7 @@ public interface IProteomicsDataApiFacade
/**
* Returns all experiments of specified type which the specified user is allowed to read.
*/
- public List<Experiment> listSearchExperiments(String sessionToken, String userID, String experimentTypeCode);
+ public List<Experiment> listExperiments(String sessionToken, String userID, String experimentTypeCode);
/**
* Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS
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
deleted file mode 100644
index 866613a3f1838347cf9262c5888ec1ab4528b3b3..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/IRawDataApiFacade.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * 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.generic.shared.api.v1.dto.Project;
-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
- */
-@Deprecated
-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. Only the most recent data sets of specified type are processed.
- */
- public void processingRawData(String userID, String dataSetProcessingKey,
- long[] rawDataSampleIDs, String dataSetType);
-
- /**
- * Returns all projects where the specified user has USER access rights.
- */
- public List<Project> listProjects(String userID);
-
- /**
- * Logs current user out.
- */
- public void logout();
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
index f3b2a30ce23c1710aca6fdc7ee8fbab6d8dd7c05..f31a9c98633f19627aedeb8e94929ca775a51349 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiFacade.java
@@ -110,10 +110,10 @@ class ProteomicsDataApiFacade implements IProteomicsDataApiFacade
return service.listSearchExperiments(sessionToken, userID);
}
- public List<Experiment> listSearchExperiments(String sessionToken, String userID,
+ public List<Experiment> listExperiments(String sessionToken, String userID,
String experimentTypeCode)
{
- return service.listSearchExperiments(sessionToken, userID, experimentTypeCode);
+ return service.listExperiments(sessionToken, userID, experimentTypeCode);
}
public void processSearchData(String userID, String dataSetProcessingKey,
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index 2627bf740c01ba4d257988e8181e67ec890d5e8e..ba4b3efca6417b3e337360f41887983a1d9c8130 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -152,7 +152,7 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
processDataSets(session, dataSetProcessingKey, dataSetCodes, new HashMap<String, String>());
}
- public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode)
+ public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode)
{
checkSession(sessionToken);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
index 80fcc8c6c32afc06be4a71636dfc0f22e1179ef5..74137fa1cf78210fac628e1bea55ec807105d483 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalLogger.java
@@ -63,7 +63,7 @@ class ProteomicsDataServiceInternalLogger extends AbstractServerLogger implement
dataSetCodes.size());
}
- public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode)
+ public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode)
{
logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
return null;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
index e01051d6a906a5bdfa6917dcc042f78aeeef7f32..1bf3caf8b2d84c1d0bb38f6a2bac4b5136f908f8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
@@ -230,17 +230,17 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
String sessionToken, String userID)
{
- return listSearchExperiments(sessionToken, userID, MS_SEARCH);
+ return listExperiments(sessionToken, userID, MS_SEARCH);
}
- public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listSearchExperiments(
+ public List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> listExperiments(
String sessionToken, String userID, String experimentTypeCode)
{
checkSession(sessionToken);
SessionContextDTO session = login(userID);
try
{
- List<Experiment> experiments = service.listSearchExperiments(session.getSessionToken(), experimentTypeCode);
+ List<Experiment> experiments = service.listExperiments(session.getSessionToken(), experimentTypeCode);
List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> result =
new ArrayList<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment>();
for (Experiment experiment : experiments)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
index bb22a28bf97065f17349f90e3ae03b0fbc5975d2..51a70117edf78c8d3db29b94cefccedf060f3856 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceLogger.java
@@ -79,7 +79,7 @@ class ProteomicsDataServiceLogger extends AbstractServerLogger implements IProte
return null;
}
- public List<Experiment> listSearchExperiments(String sessionToken, String userID,
+ public List<Experiment> listExperiments(String sessionToken, String userID,
String experimentTypeCode)
{
logAccess(sessionToken, "list_search_experiments", "EXPERIMENT_TYPE(%s)", experimentTypeCode);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
index e9917e1a3ba0dbb3f8029f2f482ee54bb3093a59..a2ac631dfcfe0ee8e0b000b576a7d056849a5c2f 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IProteomicsDataServiceInternal.java
@@ -63,7 +63,7 @@ public interface IProteomicsDataServiceInternal extends IServer
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
@ReturnValueFilter(validatorClass = ExperimentValidator.class)
- public List<Experiment> listSearchExperiments(String sessionToken, String experimentTypeCode);
+ public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode);
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
index 1197b137e3cd61ac5726759dd31bb252771f4f1a..c254a6bda06f151e6508a3d75d5d17feb9d8ff37 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/IProteomicsDataService.java
@@ -110,7 +110,7 @@ public interface IProteomicsDataService extends IRpcService
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
- public List<Experiment> listSearchExperiments(String sessionToken, String userID, String experimentTypeCode);
+ public List<Experiment> listExperiments(String sessionToken, String userID, String experimentTypeCode);
/**
* Processes the data sets of specified experiments of type <tt>MS_SEARCH</tt> by the DSS
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
index e6d416959fb67e6c889413659a5fe08adb2c1feb..c34c3ae300e05745c45e06eb87e3fd68e098da51 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_TYPE_CODE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.EXPERIMENT_PROPERTIES_FILE_NAME_KEY;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.EXPERIMENT_TYPE_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES;
import java.io.File;
@@ -73,13 +75,40 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
context.assertIsSatisfied();
}
+ @Test
+ public void testWithNonDefaultExperimentTypeAndPropertiesFileName()
+ {
+ String propertiesFile = "my.properties";
+ FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
+ Properties properties = new Properties();
+ String experimentType = "MY_EXPERIMENT";
+ properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
+ properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
+ prepare(experimentType);
+ context.checking(new Expectations()
+ {
+ {
+ one(service).registerExperiment(with(any(NewExperiment.class)));
+ }
+ });
+
+ IDataSetInfoExtractor extractor = createExtractor(properties);
+
+ DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
+
+ assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
+ assertEquals("[1, 2, 3, 4]", info.getParentDataSetCodes().toString());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testRegistrationWithOneMandatoryProperty()
{
FileUtilities.writeToFile(new File(dataSet,
DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME),
"answer=42\nblabla=blub\n" + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
- prepare();
+ prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
context.checking(new Expectations()
{
@@ -121,7 +150,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testRegistrationWithMissingMandatoryProperty()
{
- prepare();
+ prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
IDataSetInfoExtractor extractor = createExtractor(new Properties());
try
@@ -136,7 +165,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
context.assertIsSatisfied();
}
- private void prepare()
+ private void prepare(final String experimentType)
{
context.checking(new Expectations()
{
@@ -144,7 +173,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
one(service).drawANewUniqueID();
will(returnValue(4711L));
- one(service).getExperimentType(DEFAULT_EXPERIMENT_TYPE_CODE);
+ one(service).getExperimentType(experimentType);
ExperimentType type = new ExperimentType();
ExperimentTypePropertyType etpt = new ExperimentTypePropertyType();
PropertyType propertyType = new PropertyType();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index 71bec3a662c3ad0437c32fc69523c88b47368eec..eaaf148e7e8c2daf3c8ffcc0612ef0c473f66bde 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -137,14 +137,14 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
}
@Test
- public void testListSearchExperiments()
+ public void testListExperiments()
{
prepareGetSession();
final ExperimentPE e1 = experiment(1);
final ExperimentPE e2 = experiment(2, "a");
- prepareListSearchExperiments(e1, e2);
+ prepareListExperiments(e1, e2);
- List<Experiment> list = service.listSearchExperiments(SESSION_TOKEN, EXPERIMENT_TYPE);
+ List<Experiment> list = service.listExperiments(SESSION_TOKEN, EXPERIMENT_TYPE);
assertEquals("HOME_DATABASE:/G/P/e1", list.get(0).getIdentifier());
assertEquals(1, list.get(0).getRegistrationDate().getTime());
@@ -264,7 +264,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
return session;
}
- private void prepareListSearchExperiments(final ExperimentPE... experiments)
+ private void prepareListExperiments(final ExperimentPE... experiments)
{
context.checking(new Expectations()
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
index 7081ab7b7ee830458dd85e1bdd2a85765377adf9..8400078039096c118ecb39c71168e11c91b20a58 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataServiceTest.java
@@ -297,7 +297,7 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
}
@Test
- public void testListSearchExperiments()
+ public void testListExperiments()
{
prepareGetSession();
prepareLoginLogout(session2);
@@ -322,13 +322,13 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(internalService).listSearchExperiments(session2.getSessionToken(), MS_SEARCH);
+ one(internalService).listExperiments(session2.getSessionToken(), MS_SEARCH);
will(returnValue(Arrays.asList(e)));
}
});
List<ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment> experiments =
- service.listSearchExperiments(SESSION_TOKEN, "abc");
+ service.listExperiments(SESSION_TOKEN, "abc", MS_SEARCH);
assertEquals(e.getId().longValue(), experiments.get(0).getId());
assertEquals(e.getCode(), experiments.get(0).getCode());
@@ -353,15 +353,16 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
{
prepareGetSession();
prepareLoginLogout(session2);
- final long[] ids = new long[] {42};
+ final long[] ids = new long[] { 42 };
context.checking(new Expectations()
{
{
- one(internalService).processProteinResultDataSets(session2.getSessionToken(), "dsp1", MS_SEARCH, ids);
+ one(internalService).processProteinResultDataSets(session2.getSessionToken(),
+ "dsp1", MS_SEARCH, ids);
}
});
- service.processSearchData(SESSION_TOKEN, "abc", "dsp1", ids);
+ service.processProteinResultDataSets(SESSION_TOKEN, "abc", "dsp1", MS_SEARCH, ids);
context.assertIsSatisfied();
}