diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/Constants.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/Constants.java
new file mode 100644
index 0000000000000000000000000000000000000000..09ec8935ee1f5a7b8ecb99a9878c7cc5829d9400
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/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.etlserver;
+
+/**
+ *
+ *
+ * @author Izabela Adamczyk
+ */
+public class Constants
+{
+
+ public static final String ERROR_MARKER_FILE = "_delete_me_after_correcting_errors";
+ public static final String USER_LOG_FILE = "error-log.txt";
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f5eadb43f88064b8ecc6cd4f5b137dce53f264b
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/SampleRegisteringDropbox.java
@@ -0,0 +1,224 @@
+/*
+ * 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.etlserver;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.parser.GlobalProperties;
+import ch.systemsx.cisd.openbis.generic.shared.parser.GlobalPropertiesLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser.BatchSamplesOperation;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser.SampleCodeGenerator;
+
+/**
+ * Registers samples from provided file. No data sets are created.
+ *
+ * @author Izabela Adamczyk
+ */
+public class SampleRegisteringDropbox implements IDataSetHandler
+// WORKAROUND: {@link IDataSetHandler} has been used because it's the
+// fastest way to implement required feature (sample batch registration via dropbox). It would
+// be better to be able to configure a special dropbox directly in openBIS.
+{
+
+ private static final String USER_KEY = "USER";
+
+ private static final String DEFAULT_SPACE_KEY = "DEFAULT_SPACE";
+
+ private static final String SAMPLE_TYPE_KEY = "SAMPLE_TYPE";
+
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ SampleRegisteringDropbox.class);
+
+ private final IEncapsulatedOpenBISService service;
+
+ private String logDir;
+
+ private String samplePrefix;
+
+ public SampleRegisteringDropbox(Properties parentProperties, IDataSetHandler delegator,
+ IEncapsulatedOpenBISService service)
+ {
+ this.service = service;
+ Properties specificProperties = getSpecificProperties(parentProperties);
+ logDir = PropertyUtils.getMandatoryProperty(specificProperties, "error-log-dir");
+ samplePrefix = PropertyUtils.getProperty(specificProperties, "sample-code-prefix", "S");
+ }
+
+ private static Properties getSpecificProperties(Properties properties)
+ {
+ return ExtendedProperties.getSubset(properties, IDataSetHandler.DATASET_HANDLER_KEY + '.',
+ true);
+ }
+
+ public List<DataSetInformation> handleDataSet(File file)
+ {
+ File marker = new File(file.getParent(), createErrorMarkerFileName(file));
+ File logFile = new File(new File(logDir), createErrorLogFileName(file));
+ try
+ {
+ if (marker.exists())
+ {
+ return createReturnValue();
+ }
+ GlobalProperties properties = GlobalPropertiesLoader.load(file);
+ String defaultSpaceIdentifierOrNull = tryExtractSpaceIdentifier(properties);
+ String userOrNull = properties.tryGet(USER_KEY);
+ SampleType sampleType = extractSampleType(properties);
+ logGlobalPropertiesExtracted(file, defaultSpaceIdentifierOrNull, userOrNull, sampleType);
+ boolean generateCodesAutomatically = defaultSpaceIdentifierOrNull != null;
+ SampleCodeGenerator sampleCodeGeneratorOrNull =
+ tryCreateCodeGenrator(generateCodesAutomatically);
+ NamedInputStream stream =
+ new NamedInputStream(new FileInputStream(file), file.getName(),
+ FileUtils.readFileToByteArray(file));
+ BatchSamplesOperation info =
+ SampleUploadSectionsParser.prepareSamples(sampleType, Arrays.asList(stream),
+ defaultSpaceIdentifierOrNull, sampleCodeGeneratorOrNull, true,
+ BatchOperationKind.REGISTRATION);
+ logSamplesExtracted(file, info);
+ service.registerSamples(info.getSamples(), userOrNull);
+ logSamplesRegistered(file, info);
+ } catch (Exception ex)
+ {
+
+ String message = ex.getMessage();
+ try
+ {
+ FileUtils.touch(marker);
+ FileUtils.writeStringToFile(logFile, message);
+ } catch (IOException logEx)
+ {
+ operationLog.error(String.format(
+ "Could not write to error log: [%s]. Message: [%s]", logFile.getPath(),
+ message));
+ }
+ return createReturnValue();
+ }
+ FileOperations.getMonitoredInstanceForCurrentThread().deleteRecursively(file);
+ logFileDeletion(file);
+ return createReturnValue();
+ }
+
+ private String createErrorLogFileName(File file)
+ {
+ return file.getName() + "_" + Constants.USER_LOG_FILE;
+ }
+
+ private String createErrorMarkerFileName(File file)
+ {
+ return file.getName() + Constants.ERROR_MARKER_FILE;
+ }
+
+ private ArrayList<DataSetInformation> createReturnValue()
+ {
+ return new ArrayList<DataSetInformation>();
+ }
+
+ private void logSamplesRegistered(File file, BatchSamplesOperation info)
+ {
+ String message =
+ String.format("%s samples extracted from file '%s' and registered",
+ info.getCodes().length, file.getName());
+ operationLog.info(message);
+ }
+
+ private void logFileDeletion(File file)
+ {
+ String message =
+ String.format("Deleting file '%s' after successfull registration of samples",
+ file.getName());
+ operationLog.debug(message);
+ }
+
+ private void logSamplesExtracted(File file, BatchSamplesOperation info)
+ {
+ String message =
+ String.format("Samples found in file '%s': %s", file.getName(),
+ info.getCodes().length);
+ operationLog.debug(message);
+ }
+
+ private void logGlobalPropertiesExtracted(File file, String defaultSpaceIdentifierOrNull,
+ String userOrNull, SampleType sampleType)
+ {
+ String message =
+ String.format(
+ "Global properties extracted from file '%s': SAMPLE_TYPE(%s) DEFAULT_SPACE(%s) USER(%s)",
+ file.getName(), sampleType, defaultSpaceIdentifierOrNull, userOrNull);
+ operationLog.debug(message);
+ }
+
+ private SampleType extractSampleType(GlobalProperties properties)
+ {
+ String sampleTypeCode = properties.get(SAMPLE_TYPE_KEY);
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(sampleTypeCode);
+ return sampleType;
+ }
+
+ private String tryExtractSpaceIdentifier(GlobalProperties properties)
+ {
+ String spaceCodeOrNull = properties.tryGet(DEFAULT_SPACE_KEY);
+ if (spaceCodeOrNull == null)
+ {
+ return null;
+ }
+ return new SpaceIdentifier(DatabaseInstanceIdentifier.createHome(), spaceCodeOrNull)
+ .toString();
+ }
+
+ private SampleCodeGenerator tryCreateCodeGenrator(boolean generateCodesAutomatically)
+ {
+ if (generateCodesAutomatically)
+ {
+ return new SampleCodeGenerator()
+ {
+
+ public List<String> generateCodes(int size)
+ {
+ return service.generateCodes(samplePrefix, size);
+ }
+ };
+ } else
+ {
+ return null;
+ }
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 758805d7d0c904f0eaa3f9d69e154a631fef9f26..151975c2db01b93b4df55506d20ea13e7aaa0170 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -48,6 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
@@ -79,8 +80,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISService, FactoryBean
{
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, EncapsulatedOpenBISService.class);
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ EncapsulatedOpenBISService.class);
private final IETLLIMSService service;
@@ -436,6 +437,22 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
}
}
+ synchronized public void registerSamples(List<NewSamplesWithTypes> newSamples,
+ String userIDOrNull) throws UserFailureException
+ {
+ assert newSamples != null : "Unspecified samples.";
+
+ checkSessionToken();
+ try
+ {
+ service.registerSamples(sessionToken, newSamples, userIDOrNull);
+ } catch (final InvalidSessionException ex)
+ {
+ authenticate();
+ service.registerSamples(sessionToken, newSamples, userIDOrNull);
+ }
+ }
+
synchronized public long registerSample(NewSample newSample, String userIDOrNull)
throws UserFailureException
{
@@ -766,4 +783,22 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
return service.tryGetDataSetForServer(sessionToken, dataSetCode);
}
+ public List<String> generateCodes(String prefix, int size)
+ {
+ checkSessionToken();
+ try
+ {
+ return primGenerateCodes(prefix, size);
+ } catch (final InvalidSessionException ex)
+ {
+ authenticate();
+ return primGenerateCodes(prefix, size);
+ }
+ }
+
+ private List<String> primGenerateCodes(String prefix, int size)
+ {
+ return service.generateCodes(sessionToken, prefix, size);
+ }
+
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index c5c50e161fd96158b92ec7f34d89095b778e0a5f..fd0e21f0f964d55cdfc88d5f9ff4e633f5649d90 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
@@ -162,6 +163,12 @@ public interface IEncapsulatedOpenBISService
public long registerSample(final NewSample newSample, String userIDOrNull)
throws UserFailureException;
+ /**
+ * Registers samples in batches.
+ */
+ public void registerSamples(List<NewSamplesWithTypes> newSamples, String userIDOrNull)
+ throws UserFailureException;
+
/**
* Updates sample specified by the argument.
*/
@@ -210,6 +217,11 @@ public interface IEncapsulatedOpenBISService
*/
public long drawANewUniqueID();
+ /**
+ * Creates a new unique ID which can be used to create codes which are guaranteed to be unique.
+ */
+ public List<String> generateCodes(String prefix, int size);
+
/**
* Returns the version of the service.
*/
@@ -232,7 +244,7 @@ public interface IEncapsulatedOpenBISService
public void updateDataSet(String code, List<NewProperty> properties, SpaceIdentifier space)
throws UserFailureException;
- //
+ //
// Archiving
//
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
index e8d636d4ea0fa1586cacf178da5f72ccedcfa053..68233a4fdeedb2687440128afed8cce2e7c12e76 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/CifexStorageProcessorTest.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.etlserver.DefaultStorageProcessorTest.TestProcedureAndDa
*/
public class CifexStorageProcessorTest extends AbstractFileSystemTestCase
{
- // TODO 2009-07-09 Izabela Adamczyk: Add more test cases
+ // TODO 2009-07-09, IA: Add more test cases
private final static ITypeExtractor TYPE_EXTRACTOR = new TestProcedureAndDataTypeExtractor();
@@ -74,9 +74,11 @@ public class CifexStorageProcessorTest extends AbstractFileSystemTestCase
assertEquals(false, incomingDataSetDirectory.exists());
assertEquals(true, storeData.isDirectory());
assertEquals(rootDir.getAbsolutePath(), storeData.getAbsolutePath());
- assertEquals("hello world", FileUtilities.loadToString(
- new File(storeData, DefaultStorageProcessor.ORIGINAL_DIR + "/incoming/read.me"))
- .trim());
+ assertEquals(
+ "hello world",
+ FileUtilities.loadToString(
+ new File(storeData, DefaultStorageProcessor.ORIGINAL_DIR
+ + "/incoming/read.me")).trim());
}
@Test
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ProjectSelectionTreeGridContainer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ProjectSelectionTreeGridContainer.java
index 4764a35d88cc1df1b45b786a9d55c7867d7c0b4f..fafeb7b0c1fb10a6cb06746caa7e878370e20071 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ProjectSelectionTreeGridContainer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/experiment/ProjectSelectionTreeGridContainer.java
@@ -218,13 +218,6 @@ public final class ProjectSelectionTreeGridContainer extends LayoutContainer imp
href);
}
};
- // TODO 2010-06-14, IA: try to adjust the size and use the info icon
- // AbstractImagePrototype infoIcon =
- // AbstractImagePrototype.create(viewContext.getImageBundle()
- // .getInfoIcon());
- //
- // final Widget detailsLink =
- // LinkRenderer.getLinkWidgetWithHtml(listener, href, infoIcon.getHTML());
final Widget detailsLink =
LinkRenderer.getLinkWidget(viewContext
.getMessage(Dict.PROJECT_SELECTOR_DETAILS_LINK_LABEL),
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
index 413f85f3fb842a092db98837800139cf99f53ddd..d8675e5f5d05e841dfa4f5fe2c29fb85406a17f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/CommonClientService.java
@@ -157,6 +157,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
/**
* The {@link ICommonClientService} implementation.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
index 00501c2733f19e508ef9b124df7b396581610b1d..b13229d1551f3093c5fd895a0aa691ee281e137c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractCommonServer.java
@@ -80,8 +80,8 @@ abstract class AbstractCommonServer<T extends IServer> extends AbstractServer<T>
if (unknownUsers.size() > 0)
{
throw UserFailureException.fromTemplate(
- "Following persons unknown by the authentication service: [%s]", StringUtils
- .join(userIDs, ","));
+ "Following persons unknown by the authentication service: [%s]",
+ StringUtils.join(userIDs, ","));
} else
{
return newPersons;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
index 12d0eec08d76d31850dfd122a28cb3d9c0a47ded..3503c7f577d47d8069c809df7559a64050dc3794 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/AbstractServer.java
@@ -41,7 +41,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DisplaySettings;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GridCustomColumn;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
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.GridCustomColumnPE;
@@ -55,6 +58,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleSession;
import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomColumnTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
/**
* An <i>abstract</i> {@link IServer} implementation.
@@ -83,11 +87,11 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
@Resource(name = ComponentNames.REMOTE_HOST_VALIDATOR)
private IRemoteHostValidator remoteHostValidator;
-
+
protected AbstractServer()
{
- operationLog.info(String.format("Creating new '%s' implementation: '%s'.", IServer.class
- .getSimpleName(), getClass().getName()));
+ operationLog.info(String.format("Creating new '%s' implementation: '%s'.",
+ IServer.class.getSimpleName(), getClass().getName()));
}
protected AbstractServer(final ISessionManager<Session> sessionManager,
@@ -108,7 +112,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
this.sampleTypeSlaveServerPlugin = sampleTypeSlaveServerPlugin;
this.dataSetTypeSlaveServerPlugin = dataSetTypeSlaveServerPlugin;
}
-
+
public final void setSampleTypeSlaveServerPlugin(
ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin)
{
@@ -173,7 +177,7 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
}
return person;
}
-
+
protected final PersonPE getSystemUser()
{
return getSystemUser(daoFactory.getPersonDAO().listPersons());
@@ -410,4 +414,30 @@ public abstract class AbstractServer<T> extends AbstractServiceWithLogger<T> imp
HibernateUtils.initialize(person.getAllPersonRoles());
session.setPerson(person);
}
+
+ protected void registerSamples(final Session session,
+ final NewSamplesWithTypes newSamplesWithType, PersonPE registratorOrNull)
+ {
+ final SampleType sampleType = newSamplesWithType.getSampleType();
+ final List<NewSample> newSamples = newSamplesWithType.getNewSamples();
+ assert sampleType != null : "Unspecified sample type.";
+ assert newSamples != null : "Unspecified new samples.";
+
+ // Does nothing if samples list is empty.
+ if (newSamples.size() == 0)
+ {
+ return;
+ }
+ ServerUtils.prevalidate(newSamples, "sample");
+ final String sampleTypeCode = sampleType.getCode();
+ final SampleTypePE sampleTypePE =
+ getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
+ if (sampleTypePE == null)
+ {
+ throw UserFailureException.fromTemplate("Sample type with code '%s' does not exist.",
+ sampleTypeCode);
+ }
+ getSampleTypeSlaveServerPlugin(sampleTypePE).registerSamples(session, newSamples,
+ registratorOrNull);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index f2536d19ab7a3ac886f9462ef8e6046bd6729f1a..06790e63b4511bbfb2a4fd7a741d7f07f96ea92a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
@@ -64,6 +65,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCrite
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyTypeWithVocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -102,12 +104,12 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.DatabaseInstanceTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
@@ -506,6 +508,20 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return experimentBO.getExperiment().getId();
}
+ public void registerSamples(String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType, String userIDOrNull)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ PersonPE registratorOrNull =
+ userIDOrNull != null ? getOrCreatePerson(sessionToken, userIDOrNull) : null;
+ for (NewSamplesWithTypes samples : newSamplesWithType)
+ {
+ registerSamples(session, samples, registratorOrNull);
+ }
+ }
+
public long registerSample(String sessionToken, NewSample newSample, String userIDOrNull)
throws UserFailureException
{
@@ -753,4 +769,15 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return VocabularyTermTranslator.translateTerms(vocabularyOrNull.getTerms());
}
+ public List<String> generateCodes(String sessionToken, String prefix, int number)
+ {
+ checkSession(sessionToken);
+ ArrayList<String> result = new ArrayList<String>();
+ for (int i = 0; i < number; i++)
+ {
+ result.add(prefix + daoFactory.getCodeSequenceDAO().getNextCodeSequenceId());
+ }
+ return result;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index f2550a915474212e6b4b21b53bacffa72f2a14f2..d96caa707fedb168355c06ae759cb2393ad93d44 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
@@ -93,9 +94,9 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
sessionToken,
"registerDataStoreServer",
"CODE(%s) DOWNLOAD-URL(%s) PORT(%s) DSS-TOKEN(%s) REPORTING_PLUGINS(%s), PROCESSING_PLUGINS(%s)",
- code, downloadUrl, port, dssSessionToken, services
- .getReportingServiceDescriptions(), services
- .getProcessingServiceDescriptions());
+ code, downloadUrl, port, dssSessionToken,
+ services.getReportingServiceDescriptions(),
+ services.getProcessingServiceDescriptions());
}
public long registerSample(String sessionToken, NewSample newSample, String userIDOrNull)
@@ -313,4 +314,33 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
return null;
}
+ public void registerSamples(String sessionToken, List<NewSamplesWithTypes> newSamplesWithType,
+ String userIdOrNull) throws UserFailureException
+ {
+
+ logTracking(sessionToken, "registerSamples", "NO_OF_SAMPLES(%s) USER(%s)",
+ print(newSamplesWithType), userIdOrNull);
+
+ }
+
+ private String print(List<NewSamplesWithTypes> newSamplesWithType)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (NewSamplesWithTypes samples : newSamplesWithType)
+ {
+ if (sb.length() != 0)
+ {
+ sb.append(", ");
+ }
+ sb.append(samples.getSampleType().getCode());
+ sb.append(":").append(samples.getNewSamples().size());
+ }
+ return sb.toString();
+ }
+
+ public List<String> generateCodes(String sessionToken, String prefix, int number)
+ {
+ logAccess(sessionToken, "generateCodes", "PREFIX(%s) NUMBER(%s)", prefix, number);
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleBatchRegistration.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleBatchRegistration.java
index 5e1d825ca902827a04707e1da8b898d0484fb779..b82aead9cbf8748974b2040fed0a41641fceb183 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleBatchRegistration.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/SampleBatchRegistration.java
@@ -20,6 +20,7 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* {@link IBatchOperation} registering samples.
@@ -32,15 +33,19 @@ public class SampleBatchRegistration implements IBatchOperation<NewSample>
private final List<NewSample> entities;
- public SampleBatchRegistration(ISampleTable businessTable, List<NewSample> entities)
+ private final PersonPE registratorOrNull;
+
+ public SampleBatchRegistration(ISampleTable businessTable, List<NewSample> entities,
+ PersonPE registratorOrNull)
{
this.businessTable = businessTable;
this.entities = entities;
+ this.registratorOrNull = registratorOrNull;
}
public void execute(List<NewSample> batch)
{
- businessTable.prepareForRegistration(batch);
+ businessTable.prepareForRegistration(batch, registratorOrNull);
businessTable.save();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index a08a01911963afb0119d9ac5df8c05aa042df7de..a4dfef76d3ae95f982f602ea0126dcaadc23ef10 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RelationshipTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -109,7 +110,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
final SamplePE createSample(final NewSample newSample,
Map<String, SampleTypePE> sampleTypeCacheOrNull,
Map<SampleOwnerIdentifier, SampleOwner> sampleOwnerCacheOrNull,
- Map<String, ExperimentPE> experimentCacheOrNull) throws UserFailureException
+ Map<String, ExperimentPE> experimentCacheOrNull, PersonPE registratorOrNull)
+ throws UserFailureException
{
final SampleIdentifier sampleIdentifier =
SampleIdentifierFactory.parse(newSample.getIdentifier());
@@ -130,7 +132,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
final SamplePE samplePE = new SamplePE();
samplePE.setExperiment(experimentPE);
samplePE.setCode(sampleIdentifier.getSampleSubCode());
- samplePE.setRegistrator(findRegistrator());
+ PersonPE registrator = registratorOrNull != null ? registratorOrNull : findRegistrator();
+ samplePE.setRegistrator(registrator);
samplePE.setSampleType(sampleTypePE);
samplePE.setSpace(sampleOwner.tryGetSpace());
samplePE.setDatabaseInstance(sampleOwner.tryGetDatabaseInstance());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
index 06c5266bc00326e09957e4826c4f916a56bef7b4..edf03ef6e9e455e23b74b9926f9cd96cd69e3d81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
@@ -22,6 +22,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -47,7 +48,8 @@ public interface ISampleTable
/**
* Prepares given samples for registration and stores them in this table.
*/
- public void prepareForRegistration(List<NewSample> newSamples) throws UserFailureException;
+ public void prepareForRegistration(List<NewSample> newSamples, PersonPE registratorOrNull)
+ throws UserFailureException;
/**
* Prepares given samples for update and stores them in this table.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 1093432bd17a6633bff5fbfb8a3aa5447c29e797..7b87d8daa5004351006e9468d853e7c29aa524a7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -128,7 +128,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
{
assert newSample != null : "Unspecified new sample.";
- sample = createSample(newSample, null, null, null);
+ sample = createSample(newSample, null, null, null, null);
dataChanged = true;
onlyNewSamples = true;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index aaf147b7582b25515199d1034bae46cabed0ef40..10d9f665274524a69485ce7cb737a42300e349e4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -165,7 +165,8 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
return samples;
}
- public void prepareForRegistration(List<NewSample> newSamples) throws UserFailureException
+ public void prepareForRegistration(List<NewSample> newSamples, PersonPE registratorOrNull)
+ throws UserFailureException
{
onlyNewSamples = true;
samples = new ArrayList<SamplePE>();
@@ -178,7 +179,7 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
new HashMap<SampleOwnerIdentifier, SampleOwner>();
for (NewSample sample : newSamples)
{
- add(sample, sampleTypeCache, sampleOwnerCache, experimentCache);
+ add(sample, sampleTypeCache, sampleOwnerCache, experimentCache, registratorOrNull);
}
setBatchUpdateMode(false);
@@ -186,10 +187,12 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
private void add(final NewSample newSample, final Map<String, SampleTypePE> sampleTypeCache,
final Map<SampleOwnerIdentifier, SampleOwner> sampleOwnerCache,
- Map<String, ExperimentPE> experimentCache) throws UserFailureException
+ Map<String, ExperimentPE> experimentCache, PersonPE registratorOrNull)
+ throws UserFailureException
{
assert newSample != null : "Unspecified new sample.";
- samples.add(createSample(newSample, sampleTypeCache, sampleOwnerCache, experimentCache));
+ samples.add(createSample(newSample, sampleTypeCache, sampleOwnerCache, experimentCache,
+ registratorOrNull));
dataChanged = true;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
index 99ebea72a5d164efff21140809c609c06b3e467c..5f6f870cc51068a573b5c50540d735d074fdf4e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/ISampleTypeSlaveServerPlugin.java
@@ -21,6 +21,7 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.DAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleParentWithDerivedDTO;
@@ -46,8 +47,8 @@ public interface ISampleTypeSlaveServerPlugin
/**
* Registers given list of {@link NewSample NewSamples}.
*/
- void registerSamples(final Session session, final List<NewSample> newSamples)
- throws UserFailureException;
+ void registerSamples(final Session session, final List<NewSample> newSamples,
+ PersonPE registratorOrNUll) throws UserFailureException;
/**
* Updates given list of samples.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 9998fe1978911648af5d6510e0b7dde45d70fd69..be91421c2e9ece85c2ceeec4205169411833d24f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -26,23 +26,25 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.ISessionProvider;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampleCriteriaPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSamplesByPropertyPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewExperimentPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewSamplePredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.NewSamplesWithTypePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwnerIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleUpdatesPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SpaceIdentifierPredicate;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.SampleValidator;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
@@ -51,11 +53,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
@@ -222,10 +224,19 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = NewExperimentPredicate.class) NewExperiment experiment)
throws UserFailureException;
+ /**
+ * Registers samples in batches.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ @DatabaseUpdateModification(value = ObjectKind.SAMPLE)
+ public void registerSamples(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class) final List<NewSamplesWithTypes> newSamplesWithType,
+ String userIdOrNull) throws UserFailureException;
+
/**
* Registers a new sample.
- *
- * @return the technical ID of the new sample.
*/
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
@@ -295,7 +306,7 @@ public interface IETLLIMSService extends IServer, ISessionProvider
public void deleteDataSet(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode,
String reason) throws UserFailureException;
-
+
/**
* Checks that the user of specified session has INSTANCE_ADMIN access rights.
*/
@@ -459,4 +470,11 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode)
throws UserFailureException;
+ /**
+ * Returns a list of unique codes.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ public List<String> generateCodes(String sessionToken, String prefix, int number);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/BatchRegistrationResult.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
similarity index 86%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/BatchRegistrationResult.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
index c0e2ea35d13d1540c655b3e7c59e913bdd111e84..64a5803f3b7e8f88600e05d9c1abd553098bca81 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/BatchRegistrationResult.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BatchRegistrationResult.java
@@ -14,7 +14,9 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.client.web.client.dto;
+package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+
+import java.io.Serializable;
import com.google.gwt.user.client.rpc.IsSerializable;
@@ -24,8 +26,11 @@ import com.google.gwt.user.client.rpc.IsSerializable;
*
* @author Christian Ribeaud
*/
-public class BatchRegistrationResult implements IsSerializable
+public class BatchRegistrationResult implements IsSerializable, Serializable
{
+
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
private String fileName;
private String message;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSamplesWithTypes.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSamplesWithTypes.java
index 3c472c69c5eb5c5ed8cac505da7e1ddc7d8cc52a..6f6065a0bf8718422dff7fe61575379883678947 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSamplesWithTypes.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSamplesWithTypes.java
@@ -16,15 +16,20 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+import java.io.Serializable;
import java.util.List;
+import com.google.gwt.user.client.rpc.IsSerializable;
+
/**
* Contains a list of new samples and their type.
*
* @author Izabela Adamczyk
*/
-public class NewSamplesWithTypes
+public class NewSamplesWithTypes implements IsSerializable, Serializable
{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
SampleType sampleType;
List<NewSample> newSamples;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/BisTabFileLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
similarity index 98%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/BisTabFileLoader.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
index 3af17f97b1f01e9de2441624c90dc094b46a17d7..ea470420dc63e4db88eb5ef0df8423830dcfc489 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/BisTabFileLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisTabFileLoader.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.client.web.server;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.Reader;
import java.util.List;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.java
new file mode 100644
index 0000000000000000000000000000000000000000..c35035444ab0f699734608a637cd29368189a8a1
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalProperties.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.generic.shared.parser;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public class GlobalProperties
+{
+
+ private final Map<String, String> properties = new HashMap<String, String>();
+
+ public GlobalProperties()
+ {
+ }
+
+ /**
+ * Adds property with given key and value.Throws {@link IllegalArgumentException} if property
+ * already defined.
+ */
+ public void add(String key, String value)
+ {
+ if (properties.containsKey(key))
+ {
+ throw new IllegalArgumentException(String.format("Property '%s' defined twice.", key));
+ }
+ properties.put(key, value);
+ }
+
+ /**
+ * Returns value of given property. Throws {@link IllegalArgumentException} if property not
+ * defined.
+ */
+ public String get(String key)
+ {
+ String value = tryGet(key);
+ if (value == null)
+ {
+ throw new IllegalArgumentException(String.format("Property '%s' not defined.", key));
+ }
+ return value;
+ }
+
+ /**
+ * Returns value of given property.
+ */
+ public String tryGet(String key)
+ {
+ return properties.get(key);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..5e85cb99ec75cccc387243f81aba1aa4b9de7fee
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/GlobalPropertiesLoader.java
@@ -0,0 +1,114 @@
+/*
+ * 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.generic.shared.parser;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.LineIterator;
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * Loads global properties.
+ * <p>
+ * Global properties are defined as a comment and start with {@link #GLOBAL_PROPERTIES} followed by
+ * a new line character. Each property is defined in a separate line and has the following format:
+ * <p>
+ * # key = value
+ * </p>
+ * First line in a different format marks the end of global properties. (Empty line can be used).
+ * <p>
+ * Example:
+ * </p>
+ * </p> --- FILE ---<br>
+ * # GLOBAL_PROPERTIES: <br>
+ * # key1 = value1 <br>
+ * # key2 = value2 <br>
+ * <br>
+ * code parent experiment <br>
+ * --- EOF ---
+ *
+ * @author Izabela Adamczyk
+ */
+public class GlobalPropertiesLoader
+{
+ private static final String COMMENT_PREFIX = "#";
+
+ static String GLOBAL_PROPERTIES = "#GLOBAL_PROPERTIES:";
+
+ public static GlobalProperties load(File file) throws FileNotFoundException
+ {
+ GlobalProperties properties = new GlobalProperties();
+ InputStreamReader reader = new FileReader(file);
+ try
+ {
+ LineIterator it = IOUtils.lineIterator(reader);
+ boolean propertiesStarted = false;
+ while (it.hasNext())
+ {
+ String line = it.nextLine();
+ if (isGlobalPropertiesStarter(line))
+ {
+ propertiesStarted = true;
+ continue;
+ }
+ if (propertiesStarted)
+ {
+ String[] definitionOrNull = tryGetPropertyDefinition(line);
+ if (definitionOrNull != null)
+ {
+ properties.add(definitionOrNull[0], definitionOrNull[1]);
+ continue;
+ } else
+ {
+ return properties;
+ }
+ }
+ }
+ } finally
+ {
+ IOUtils.closeQuietly(reader);
+ }
+ return properties;
+ }
+
+ private static String[] tryGetPropertyDefinition(String line)
+ {
+ String commentPrefix = COMMENT_PREFIX;
+ if (line.startsWith(commentPrefix))
+ {
+ String[] splitted = StringUtils.split(line.substring(commentPrefix.length()), "=", 2);
+ if (splitted.length == 2)
+ {
+ String[] result = new String[2];
+ result[0] = StringUtils.trim(splitted[0]);
+ result[1] = StringUtils.trim(splitted[1]);
+ return result;
+ }
+ }
+ return null;
+ }
+
+ private static boolean isGlobalPropertiesStarter(String line)
+ {
+ return line.equals(GLOBAL_PROPERTIES);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/NamedInputStream.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
similarity index 95%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/NamedInputStream.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
index e9c2bc59aa7cf8788171280e3af0b20c998da03e..5556981bdb0bd8c0749551366314383239dc74f3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/server/NamedInputStream.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.generic.client.web.server;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.InputStream;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactory.java
similarity index 98%
rename from openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactory.java
index f997cebd8e2db3261970b621e3d21cd88b407590..41f5bbe74e6a5f90d34d51a9c54e64dedf8eb9b4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.util.ArrayList;
import java.util.List;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/SampleUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
similarity index 96%
rename from openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/SampleUploadSectionsParser.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
index 8955fccbf0d4c138782317d81ada9a19647cd4e2..47c649d5a6ecdd149c88acb7e969d05ebbcd9bc7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/SampleUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.InputStream;
import java.io.InputStreamReader;
@@ -32,10 +32,8 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.generic.client.web.server.BisTabFileLoader;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -274,8 +272,7 @@ public class SampleUploadSectionsParser
sampleSections.size() == 1 ? "" : " (section:" + fs.getSectionName() + ")";
final List<NewSample> loadedSamples =
tabFileLoader.load(new DelegatedReader(stringReader, multipartFile
- .getOriginalFilename()
- + sectionInFile));
+ .getOriginalFilename() + sectionInFile));
if (loadedSamples.size() > 0)
{
newSamples.add(new NewSamplesWithTypes(typeFromSection, loadedSamples));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
similarity index 98%
rename from openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
index 070e0ff03c684c76720b5325aca8ec781e767aeb..b9b089421beeb75f143615bf48641c1d0d4c26f8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactory.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.util.ArrayList;
import java.util.HashSet;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..e45c9057d3580f244fb96264460a9d75b6041216
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/ServerUtils.java
@@ -0,0 +1,62 @@
+/*
+ * 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.generic.shared.util;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Tools to be used by servers.
+ *
+ * @author Izabela Adamczyk
+ */
+public class ServerUtils
+{
+ /**
+ * @throws UserFailureException when list of entities contains duplicates.
+ */
+ static public <T> void prevalidate(List<T> entities, String entityName)
+ {
+ Collection<T> duplicated = extractDuplicatedElements(entities);
+ if (duplicated.size() > 0)
+ {
+ throw UserFailureException.fromTemplate("Following %s(s) '%s' are duplicated.",
+ entityName, CollectionUtils.abbreviate(duplicated, 20));
+ }
+ }
+
+ private static <T> Collection<T> extractDuplicatedElements(List<T> entities)
+ {
+ Set<T> entitiesSet = new HashSet<T>(entities);
+ Collection<T> duplicated = new ArrayList<T>();
+ for (T entity : entities)
+ {
+ // this element must have been duplicated
+ if (entitiesSet.remove(entity) == false)
+ {
+ duplicated.add(entity);
+ }
+ }
+ return duplicated;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
index 0b4c4125f901ae01c18314b35fd3857f2aa9a1fd..1363d956e8e1c09c5ba6eb1002aea7bd0d995673 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientService.java
@@ -20,11 +20,11 @@ import java.util.Date;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DataSetUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SampleUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
index 382b42a679b05fe878bb209f9731e3d4bff145fb..fb626504f1a8de097998198c0d62574519340e77 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/IGenericClientServiceAsync.java
@@ -22,11 +22,11 @@ import java.util.List;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DataSetUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SampleUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetBatchUpdateForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetBatchUpdateForm.java
index dbae9debc755e2450d82034a262bc11ec7631c79..16b4e9c4478eac50f709390f657c730e0c59d804 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetBatchUpdateForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/dataset/GenericDataSetBatchUpdateForm.java
@@ -41,8 +41,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.L
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractExperimentBatchRegistrationForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractExperimentBatchRegistrationForm.java
index 5cfeaac41915e64eacdf1eef22b3135daeb05de8..8f8240fa949e67e596e14512ee958e45f5d9d5f3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractExperimentBatchRegistrationForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractExperimentBatchRegistrationForm.java
@@ -41,8 +41,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.L
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
@@ -70,9 +70,9 @@ public abstract class AbstractExperimentBatchRegistrationForm extends AbstractRe
private final BatchOperationKind batchOperationKind;
- public AbstractExperimentBatchRegistrationForm(IViewContext<IGenericClientServiceAsync> viewContext,
- ExperimentType type, BatchOperationKind batchOperationKind,
- String sessionKey)
+ public AbstractExperimentBatchRegistrationForm(
+ IViewContext<IGenericClientServiceAsync> viewContext, ExperimentType type,
+ BatchOperationKind batchOperationKind, String sessionKey)
{
super(viewContext.getCommonViewContext(), createId(sessionKey));
this.viewContext = viewContext;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/AbstractMaterialBatchRegistrationForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/AbstractMaterialBatchRegistrationForm.java
index add53daff630c8b2c873fc95c150b5e3358b32cb..d3632a87fb5a716422c5c570cf39eb978a8f00f4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/AbstractMaterialBatchRegistrationForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/AbstractMaterialBatchRegistrationForm.java
@@ -42,8 +42,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.L
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractRegistrationForm;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
index 9ea7206eadddb5dd404df199e27eaaf77ac7b599..06096b580356e111f0b2a488cc5b51571fc2120d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchRegistrationForm.java
@@ -37,8 +37,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.GroupSe
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CheckBoxField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchUpdateForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchUpdateForm.java
index 3a05e7f142ab11da2c48644f79a84e67c07c0718..9302a9218c83e84b451b9f5f7896f869d3a90421 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchUpdateForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleBatchUpdateForm.java
@@ -43,8 +43,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.Abstrac
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.GroupSelectionWidget;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.file.BasicFileFieldManager;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.WindowUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
index 9a513af115f0a031607d9d8496a2c8ccc5d5de26..9b9c6367a817e4d93619ef552f2465ee99a95eef 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
@@ -26,10 +26,10 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.generic.client.web.server.BisTabFileLoader;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.NewDataSetParserObjectFactory;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
index 733f0cbec5f49682eed81e6b686fded46f5ce2fb..7a2ce897af5e36e30c2d153ec0980fbdb2920927 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
@@ -27,10 +27,10 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.generic.client.web.server.BisTabFileLoader;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.NewBasicExperimentParserObjectFactory;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index bf839cbf8dacbc839c515c61c71bbd4641cbe8b4..8c19f982985db4e00834c9bafc2f1689a441c4b2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -33,17 +33,16 @@ import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
import ch.systemsx.cisd.common.spring.IUncheckedMultipartFile;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DataSetUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.SampleUpdates;
import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
import ch.systemsx.cisd.openbis.generic.client.web.server.AttachmentRegistrationHelper;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
import ch.systemsx.cisd.openbis.generic.client.web.server.UploadedFilesBean;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailureExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetUpdateResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
@@ -74,10 +73,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser.BatchSamplesOperation;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser.SampleCodeGenerator;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientService;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.SampleUploadSectionsParser;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.SampleUploadSectionsParser.BatchSamplesOperation;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.SampleUploadSectionsParser.SampleCodeGenerator;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
@@ -167,7 +167,6 @@ public class GenericClientService extends AbstractClientService implements IGene
{
throw UserFailureExceptionTranslator.translate(e);
}
-
}
public final List<BatchRegistrationResult> updateSamples(final SampleType sampleType,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
index 38a9d2691b22df2b57be8b84282c3b8c81c17125..ea7f61fc61df827b5867866e5aa35665e5290d13 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
@@ -11,10 +11,10 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.generic.client.web.server.BisTabFileLoader;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.NewMaterialParserObjectFactory;
public class MaterialLoader
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
index 780393ee3a05f8745e754c5d46840baa1bf75953..abc6eeff31440fc7074b743e528a480fc3baadff 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
@@ -27,10 +27,10 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
-import ch.systemsx.cisd.openbis.generic.client.web.server.BisTabFileLoader;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedBasicExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.UpdatedBasicExperimentParserObjectFactory;
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
index 6cf0ad08ee06ba7b31d6340df45d6b8c5d179fad..60dc6f2cf84563056feb79bbca92ff0bebf19d0e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleHierarchyFiller
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleParentWithDerivedDTO;
@@ -73,14 +74,14 @@ public final class GenericSampleTypeSlaveServerPlugin implements ISampleTypeSlav
return new SampleParentWithDerivedDTO(sample, generated);
}
- public final void registerSamples(final Session session, final List<NewSample> newSamples)
- throws UserFailureException
+ public final void registerSamples(final Session session, final List<NewSample> newSamples,
+ PersonPE registratorOrNUll) throws UserFailureException
{
assert session != null : "Unspecified session.";
assert newSamples != null && newSamples.size() > 0 : "Unspecified sample or empty samples.";
BatchOperationExecutor.executeInBatches(new SampleBatchRegistration(businessObjectFactory
- .createSampleTable(session), newSamples));
+ .createSampleTable(session), newSamples, registratorOrNUll));
}
public void updateSamples(Session session, List<SampleBatchUpdatesDTO> updateSamples)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 91d46c248d6aa6b511cf85af8a1d9ca0b03a94b8..8bfe51350dce3b2567b3d27c3c2f99b3c253984f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -34,7 +34,6 @@ import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
-import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
@@ -117,6 +116,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
@@ -287,7 +287,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
{
if (samples.isAllowUpdateIfExist() == false)
{
- registerSamples(session, samples);
+ registerSamples(session, samples, null);
} else
{
BatchOperationExecutor.executeInBatches(new SampleBatchRegisterOrUpdate(
@@ -338,7 +338,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
SampleRegisterOrUpdateUtil.getSamplesToUpdate(newSamples, existingSamples);
List<NewSample> samplesToRegister = new ArrayList<NewSample>(newSamples);
samplesToRegister.removeAll(samplesToUpdate);
- registerSamples(session, new NewSamplesWithTypes(sampleType, samplesToRegister));
+ registerSamples(session, new NewSamplesWithTypes(sampleType, samplesToRegister), null);
updateSamples(session, new NewSamplesWithTypes(sampleType, samplesToUpdate));
}
@@ -366,7 +366,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
final Session session = getSession(sessionToken);
for (NewSamplesWithTypes samples : newSamplesWithType)
{
- registerSamples(session, samples);
+ registerSamples(session, samples, null);
}
}
@@ -392,7 +392,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
{
return;
}
- prevalidate(newDataSets, "data set");
+ ServerUtils.prevalidate(newDataSets, "data set");
final DataSetTypePE dataSetType =
getDAOFactory().getDataSetTypeDAO().tryToFindDataSetTypeByCode(
dataSets.getDataSetType().getCode());
@@ -404,30 +404,6 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
getDataSetTypeSlaveServerPlugin(dataSetType).updateDataSets(session, newDataSets);
}
- private void registerSamples(final Session session, final NewSamplesWithTypes newSamplesWithType)
- {
- final SampleType sampleType = newSamplesWithType.getSampleType();
- final List<NewSample> newSamples = newSamplesWithType.getNewSamples();
- assert sampleType != null : "Unspecified sample type.";
- assert newSamples != null : "Unspecified new samples.";
-
- // Does nothing if samples list is empty.
- if (newSamples.size() == 0)
- {
- return;
- }
- prevalidate(newSamples, "sample");
- final String sampleTypeCode = sampleType.getCode();
- final SampleTypePE sampleTypePE =
- getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
- if (sampleTypePE == null)
- {
- throw UserFailureException.fromTemplate("Sample type with code '%s' does not exist.",
- sampleTypeCode);
- }
- getSampleTypeSlaveServerPlugin(sampleTypePE).registerSamples(session, newSamples);
- }
-
private void updateSamples(final Session session,
final NewSamplesWithTypes updatedSamplesWithType)
{
@@ -442,7 +418,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
return;
}
- prevalidate(updatedSamples, "sample");
+ ServerUtils.prevalidate(updatedSamples, "sample");
final String sampleTypeCode = sampleType.getCode();
final SampleTypePE sampleTypePE =
getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
@@ -577,7 +553,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
{
return;
}
- prevalidate(newMaterials, "material");
+ ServerUtils.prevalidate(newMaterials, "material");
final MaterialTypePE materialTypePE = findMaterialType(materialTypeCode);
final Session session = getSession(sessionToken);
IBatchOperation<NewMaterial> strategy = new IBatchOperation<NewMaterial>()
@@ -627,7 +603,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
int count;
}
final Counter counter = new Counter();
- prevalidate(newMaterials, "material");
+ ServerUtils.prevalidate(newMaterials, "material");
final Map<String/* code */, Material> existingMaterials =
listMaterials(sessionToken, materialTypeCode);
final Session session = getSession(sessionToken);
@@ -674,31 +650,6 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
return counter.count;
}
- private <T> void prevalidate(List<T> entities, String entityName)
- {
- Collection<T> duplicated = extractDuplicatedElements(entities);
- if (duplicated.size() > 0)
- {
- throw UserFailureException.fromTemplate("Following %s(s) '%s' are duplicated.",
- entityName, CollectionUtils.abbreviate(duplicated, 20));
- }
- }
-
- private static <T> Collection<T> extractDuplicatedElements(List<T> entities)
- {
- Set<T> entitiesSet = new HashSet<T>(entities);
- Collection<T> duplicated = new ArrayList<T>();
- for (T entity : entities)
- {
- // this element must have been duplicated
- if (entitiesSet.remove(entity) == false)
- {
- duplicated.add(entity);
- }
- }
- return duplicated;
- }
-
private MaterialTypePE findMaterialType(String materialTypeCode)
{
final MaterialTypePE materialTypePE =
@@ -902,7 +853,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
{
return;
}
- prevalidate(newExperiments, "experiment");
+ ServerUtils.prevalidate(newExperiments, "experiment");
final ExperimentTypePE experimentTypePE =
(ExperimentTypePE) getDAOFactory().getEntityTypeDAO(EntityKind.EXPERIMENT)
.tryToFindEntityTypeByCode(experiments.getExperimentTypeCode());
@@ -935,7 +886,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
{
return;
}
- prevalidate(newExperiments, "experiment");
+ ServerUtils.prevalidate(newExperiments, "experiment");
final ExperimentTypePE experimentTypePE =
(ExperimentTypePE) getDAOFactory().getEntityTypeDAO(EntityKind.EXPERIMENT)
.tryToFindEntityTypeByCode(experiments.getExperimentType().getCode());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
similarity index 99%
rename from openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java
rename to openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
index 200f3e5436cea21a2b4da9bc9f85cc01c7789d73..47ba5f7a534ca68ebfe2743a27ce5ab14c15d195 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/NewSampleParserObjectFactoryTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
similarity index 97%
rename from openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
rename to openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
index ea811f8ad25471b9de2dd394401ef36e273090f3..476b21033f47cd29ee3e6c2b2bd7baa100f2f77e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/parser/UpdatedSampleParserObjectFactoryTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
+package ch.systemsx.cisd.openbis.generic.shared.parser;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedSample;
+import ch.systemsx.cisd.openbis.generic.shared.parser.UpdatedSampleParserObjectFactory;
/**
* Test cases for corresponding {@link UpdatedSampleParserObjectFactory} class.
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
index 4f82fb95a4207cd42a2904effe8f92341df7cf2a..768ef64e93d73eeccb86076ec5c502b454e67aa6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
@@ -37,11 +37,11 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientServiceTest;
import ch.systemsx.cisd.openbis.generic.client.web.server.UploadedFilesBean;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
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;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
index 0a95c2b1939bed5aa11ff94c232815b5a1fd5e27..356a37d1dc94882c6292f87e819f9cc2f2d1bfcf 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
@@ -278,7 +278,7 @@ public final class GenericServerTest extends AbstractServerTestCase
one(sampleTypeDAO).tryFindSampleTypeByCode(sampleTypePE.getCode());
will(returnValue(sampleTypePE));
- one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples);
+ one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
}
});
createServer().registerOrUpdateSamples(SESSION_TOKEN, samplesWithTypes);
@@ -303,7 +303,7 @@ public final class GenericServerTest extends AbstractServerTestCase
one(sampleTypeDAO).tryFindSampleTypeByCode(sampleTypePE.getCode());
will(returnValue(sampleTypePE));
- one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples);
+ one(sampleTypeSlaveServerPlugin).registerSamples(SESSION, newSamples, null);
}
});
createServer().registerSamples(SESSION_TOKEN, samplesWithTypes);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/BatchMaterialRegistrationAndUpdate.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/BatchMaterialRegistrationAndUpdate.java
index cd2b960f5032562ed73cab24c4392397ef8a0cac..017bf434ede95fed54719fbe77f6c0c240136600 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/BatchMaterialRegistrationAndUpdate.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/BatchMaterialRegistrationAndUpdate.java
@@ -31,7 +31,6 @@ import javax.servlet.http.HttpSession;
import org.springframework.mock.web.MockMultipartFile;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DisplayedOrSelectedIdHolderCriteria;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.GridRowModels;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ListMaterialDisplayCriteria;
@@ -41,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.UploadedFilesBean;
import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/ExperimentRegistrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/ExperimentRegistrationTest.java
index bb568d323ad7df982a77d8ce846fdf0ee1849a4f..4e36e6a16b36447e0cf43d6aa158577640349321 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/ExperimentRegistrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/ExperimentRegistrationTest.java
@@ -28,7 +28,6 @@ import java.util.List;
import org.apache.commons.lang.StringEscapeUtils;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ListSampleDisplayCriteria;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSetWithEntityTypes;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
@@ -36,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Attachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AttachmentWithContent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
index 6beea54423e831e947dc756e06e7427758320fc3..a6df4b6c6cedb8e15c7b3fcbacfbe4a7a7bd7fa9 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetHandler.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.yeastx.etl;
-import static ch.systemsx.cisd.yeastx.etl.ConstantsYeastX.ERROR_MARKER_FILE;
-
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
@@ -34,6 +32,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.mail.MailClient;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.etlserver.Constants;
import ch.systemsx.cisd.etlserver.IDataSetHandler;
import ch.systemsx.cisd.etlserver.utils.PreprocessingExecutor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -94,8 +93,8 @@ public class BatchDataSetHandler implements IDataSetHandler
return flushErrors(batchDir, mappingFile, log);
}
- return processDatasets(batchDir, log, mappingFile.tryGetMappings(), mappingFile
- .getNotificationEmail());
+ return processDatasets(batchDir, log, mappingFile.tryGetMappings(),
+ mappingFile.getNotificationEmail());
}
private ArrayList<DataSetInformation> flushErrors(File batchDir,
@@ -114,8 +113,8 @@ public class BatchDataSetHandler implements IDataSetHandler
{
String errorMsg =
String.format("No datasets from '%s' directory can be processed because "
- + "the try to acquire write access by openBIS has failed.", batchDir
- .getName());
+ + "the try to acquire write access by openBIS has failed.",
+ batchDir.getName());
log.error(errorMsg + " Try again after some time or contact your administrator.");
log.adminError(errorMsg);
}
@@ -179,10 +178,9 @@ public class BatchDataSetHandler implements IDataSetHandler
private void logUnknownMappings(Set<String> unknownMappings, LogUtils log)
{
String unknownFiles = CollectionUtils.abbreviate(unknownMappings, -1);
- log
- .error("There are following files mentioned in the mapping file which do not exist:\n"
- + unknownFiles
- + "\nBrowse the mapping file and check if you have not misspelled some file names.");
+ log.error("There are following files mentioned in the mapping file which do not exist:\n"
+ + unknownFiles
+ + "\nBrowse the mapping file and check if you have not misspelled some file names.");
}
private void logNonWritable(File file, LogUtils log)
@@ -267,7 +265,7 @@ public class BatchDataSetHandler implements IDataSetHandler
private static boolean errorMarkerFileExists(File batchDir)
{
- return new File(batchDir, ERROR_MARKER_FILE).isFile();
+ return new File(batchDir, Constants.ERROR_MARKER_FILE).isFile();
}
private static void cleanMappingFile(File batchDir, Set<String> processedFiles, LogUtils log)
@@ -293,7 +291,7 @@ public class BatchDataSetHandler implements IDataSetHandler
private static void touchErrorMarkerFile(File batchDir, LogUtils log)
{
- File errorMarkerFile = new File(batchDir, ERROR_MARKER_FILE);
+ File errorMarkerFile = new File(batchDir, Constants.ERROR_MARKER_FILE);
if (errorMarkerFile.isFile())
{
return;
@@ -307,13 +305,11 @@ public class BatchDataSetHandler implements IDataSetHandler
}
if (ok == false)
{
- log
- .adminError("Could not create an error marker file '%s'.", errorMarkerFile
- .getPath());
+ log.adminError("Could not create an error marker file '%s'.", errorMarkerFile.getPath());
} else
{
log.warning("Correct the errors and delete the '%s' file to start processing again.",
- ERROR_MARKER_FILE);
+ Constants.ERROR_MARKER_FILE);
}
}
@@ -349,8 +345,8 @@ public class BatchDataSetHandler implements IDataSetHandler
if (ok == false)
{
LogUtils.adminWarn(
- "The directory '%s' cannot be deleted although it seems to be empty.", dir
- .getPath());
+ "The directory '%s' cannot be deleted although it seems to be empty.",
+ dir.getPath());
}
return ok;
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
index ceea820ce926a6f75fa05437b1529462f91e395b..4eb995b6de28dab8474c25f19a1caf6d44bb0ab0 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
@@ -21,10 +21,6 @@ package ch.systemsx.cisd.yeastx.etl;
*/
public class ConstantsYeastX
{
- public static final String ERROR_MARKER_FILE = "_delete_me_after_correcting_errors";
-
- public static final String USER_LOG_FILE = "error-log.txt";
-
public static final String FIAML_EXT = "fiaML";
public static final String EICML_EXT = "eicML";
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
index 188c98427847b48434615c65d240097aa480c59e..f354dc78c0c0fb5535a8971b7ed1d534e22f9892 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/LogUtils.java
@@ -29,6 +29,7 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.etlserver.Constants;
/**
* @author Tomasz Pylak
@@ -208,7 +209,7 @@ class LogUtils
private static File getUserLogFile(File loggingDir)
{
- return new File(loggingDir, ConstantsYeastX.USER_LOG_FILE);
+ return new File(loggingDir, Constants.USER_LOG_FILE);
}
public void adminError(String messageFormat, Object... arguments)
@@ -233,7 +234,7 @@ class LogUtils
public static boolean isUserLog(File file)
{
- return file.getName().equals(ConstantsYeastX.USER_LOG_FILE);
+ return file.getName().equals(Constants.USER_LOG_FILE);
}
public static boolean deleteUserLog(File loggingDir)
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
index d056bea5afad0fe6741bb04b3c130f9512afb1e1..d82fb4095520346988c56f7f69f393042b10d682 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
@@ -29,6 +29,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.test.AssertionUtil;
+import ch.systemsx.cisd.etlserver.Constants;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
/**
@@ -111,7 +112,7 @@ public class DataSetInformationParserTest extends AbstractFileSystemTestCase
private List<String> readLogFile() throws IOException, FileNotFoundException
{
- File log = new File(workingDirectory, ConstantsYeastX.USER_LOG_FILE);
+ File log = new File(workingDirectory, Constants.USER_LOG_FILE);
List<String> logLines = readLines(log);
return logLines;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
index 0c59e69802f5ae4de4cb4ad908e2616a6e61b572..3001cfc0f386fa42e33e16d1c29df426120b45ee 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
@@ -10,14 +10,14 @@ import java.util.List;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.openbis.generic.client.web.server.NamedInputStream;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchOperationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser;
+import ch.systemsx.cisd.openbis.generic.shared.parser.SampleUploadSectionsParser.BatchSamplesOperation;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.MaterialLoader;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.SampleUploadSectionsParser;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser.SampleUploadSectionsParser.BatchSamplesOperation;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.server.library_tools.ScreeningLibraryTransformer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo.RegistrationScope;