diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
index abf03fa9c840de7ebec7f372664f5bfaced69ff4..6d18fbab78a1db932af9100d75972bca7c81e8c0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
@@ -16,19 +16,30 @@
package ch.systemsx.cisd.openbis.generic.server.api.v1;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
import java.util.Map;
import javax.annotation.Resource;
+import javax.servlet.http.HttpSession;
import org.springframework.stereotype.Component;
import org.springframework.transaction.annotation.Transactional;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.InvalidSessionException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
+import ch.systemsx.cisd.openbis.common.spring.IUncheckedMultipartFile;
+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.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.exception.SampleUniqueCodeViolationExceptionAbstract;
import ch.systemsx.cisd.openbis.generic.shared.DatabaseCreateOrDeleteModification;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
@@ -38,12 +49,20 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.metaproject.IMetaprojectId;
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.DatabaseModificationKind.ObjectKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewEntitiesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+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.generic.shared.util.EntityHelper;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
/**
* @author Franz-Josef Elmer
@@ -53,7 +72,7 @@ public class GeneralInformationChangingService extends
AbstractServer<IGeneralInformationChangingService> implements
IGeneralInformationChangingService
{
- public static final int MINOR_VERSION = 3;
+ public static final int MINOR_VERSION = 4;
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
private ICommonServer server;
@@ -206,4 +225,181 @@ public class GeneralInformationChangingService extends
return MINOR_VERSION;
}
+ //
+ // <TEST IMPLEMENTATION For registerSamples>
+ //
+ @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
+ private IGenericServer genericServer;
+
+ @Resource(name = "request-context-provider")
+ @Private
+ public IRequestContextProvider requestContextProvider;
+
+ @Override
+ @Transactional(readOnly = false)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public final boolean registerSamples(
+ final String sessionToken,
+ final String sampleTypeCode,
+ final String sessionKey,
+ final String defaultGroupIdentifier)
+ {
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType> sampleTypes = server.listSampleTypes(sessionToken);
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType sampleType = null;
+ for (ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType auxSampleType : sampleTypes)
+ {
+ if (auxSampleType.getCode().equals(sampleTypeCode))
+ {
+ sampleType = auxSampleType;
+ break;
+ }
+ }
+
+ boolean isAutogenerateCodes = defaultGroupIdentifier != null;
+
+ BatchOperationKind operationKind = BatchOperationKind.REGISTRATION;
+ BatchSamplesOperation info =
+ parseSamples(sessionToken, sampleType, sessionKey, defaultGroupIdentifier, isAutogenerateCodes, true, null, operationKind);
+ try
+ {
+ genericServer.registerOrUpdateSamples(sessionToken, info.getSamples());
+ return true; // info.getResultList();
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ if (e.getCause() instanceof SampleUniqueCodeViolationExceptionAbstract)
+ {
+ SampleUniqueCodeViolationExceptionAbstract codeException = (SampleUniqueCodeViolationExceptionAbstract) e.getCause();
+
+ if (isAutogenerateCodes)
+ {
+ throw new UserFailureException(
+ String.format(
+ "Import failed because the autogenerated codes are no longer unique. Somebody has created a sample (code: %s) that matched one of the autogenerated codes. Please run the import once again.",
+ codeException.getSampleCode()));
+ } else
+ {
+ throw new UserFailureException(String.format(
+ "Import failed because sample (code: %s) already exists.",
+ codeException.getSampleCode()));
+ }
+ } else
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+ }
+
+ private BatchSamplesOperation parseSamples(
+ final String sessionToken,
+ final ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType sampleType,
+ final String sessionKey,
+ String defaultGroupIdentifier,
+ final boolean isAutoGenerateCodes,
+ final boolean allowExperiments,
+ String excelSheetName,
+ BatchOperationKind operationKind)
+ {
+ HttpSession httpSession = getHttpSession();
+ UploadedFilesBean uploadedFiles = null;
+ try
+ {
+ uploadedFiles = getUploadedFiles(sessionKey, httpSession);
+ return parseSamples(sessionToken, sampleType, httpSession, uploadedFiles, defaultGroupIdentifier,
+ isAutoGenerateCodes, allowExperiments, excelSheetName, operationKind);
+ } finally
+ {
+ cleanUploadedFiles(sessionKey, httpSession, uploadedFiles);
+ }
+ }
+
+ private BatchSamplesOperation parseSamples(
+ final String sessionToken,
+ final ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType sampleType,
+ HttpSession httpSession,
+ UploadedFilesBean uploadedFiles,
+ String defaultGroupIdentifier,
+ final boolean isAutoGenerateCodes,
+ final boolean allowExperiments,
+ String excelSheetName,
+ BatchOperationKind operationKind)
+ {
+ boolean updateExisting = (operationKind == BatchOperationKind.UPDATE);
+ SampleCodeGenerator sampleCodeGeneratorOrNull =
+ tryGetSampleCodeGenerator(sessionToken, isAutoGenerateCodes, sampleType.getGeneratedCodePrefix());
+ Collection<NamedInputStream> files = new ArrayList<NamedInputStream>(uploadedFiles.size());
+ for (IUncheckedMultipartFile f : uploadedFiles.iterable())
+ {
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
+ }
+ BatchSamplesOperation batchSamplesOperation =
+ SampleUploadSectionsParser.prepareSamples(sampleType, files,
+ defaultGroupIdentifier, sampleCodeGeneratorOrNull, allowExperiments,
+ excelSheetName, operationKind);
+ setUpdatePossibility(batchSamplesOperation.getSamples(), updateExisting);
+ return batchSamplesOperation;
+
+ }
+
+ protected static UploadedFilesBean getUploadedFiles(String sessionKey, HttpSession session)
+ {
+ if (session.getAttribute(sessionKey) == null
+ || session.getAttribute(sessionKey) instanceof UploadedFilesBean == false)
+ {
+ throw new IllegalStateException(String.format(
+ "No UploadedFilesBean object as session attribute '%s' found.", sessionKey));
+ }
+ return (UploadedFilesBean) session.getAttribute(sessionKey);
+ }
+
+ protected static void cleanUploadedFiles(final String sessionKey, HttpSession session,
+ UploadedFilesBean uploadedFiles)
+ {
+ if (uploadedFiles != null)
+ {
+ uploadedFiles.deleteTransferredFiles();
+ }
+ if (session != null)
+ {
+ session.removeAttribute(sessionKey);
+ }
+ }
+
+ private SampleCodeGenerator tryGetSampleCodeGenerator(final String sessionToken, boolean isAutoGenerateCodes,
+ final String codePrefix)
+ {
+ if (isAutoGenerateCodes)
+ {
+ return new SampleCodeGenerator()
+ {
+ @Override
+ public List<String> generateCodes(int size)
+ {
+ return genericServer.generateCodes(sessionToken, codePrefix,
+ EntityKind.SAMPLE, size);
+ }
+ };
+ } else
+ {
+ return null;
+ }
+ }
+
+ private static void setUpdatePossibility(
+ List<? extends NewEntitiesWithTypes<?, ?>> batchOperation, boolean updateExisting)
+ {
+ for (NewEntitiesWithTypes<?, ?> entitiesWithTypes : batchOperation)
+ {
+ entitiesWithTypes.setAllowUpdateIfExist(updateExisting);
+ }
+ }
+
+ protected final HttpSession getHttpSession()
+ {
+ return getOrCreateHttpSession(false);
+ }
+
+ private final HttpSession getOrCreateHttpSession(final boolean create)
+ {
+ return requestContextProvider.getHttpServletRequest().getSession(create);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
index 611dab06bf1b09f718097ccac33dcac727486a20..19d7dc24a6adacac818eda75241840c1ede92bba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
@@ -132,6 +132,18 @@ class GeneralInformationChangingServiceLogger extends AbstractServerLogger imple
abbreviate(assignments.getMaterials()));
}
+ @Override
+ public boolean registerSamples(String sessionToken, String sampleTypeCode, String sessionKey, String defaultGroupIdentifier)
+ {
+ logAccess(sessionToken, "registerSamples",
+ "sampleTypeCode(%s), sessionKey(%s), defaultGroupIdentifier(%s)",
+ sampleTypeCode,
+ sessionKey,
+ defaultGroupIdentifier);
+
+ return false;
+ }
+
@Override
public int getMajorVersion()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
index f5476a74d56f0f72713d4c678d306fa0f8405326..c6af848a4478c1027cf2d4b273228827648f9a28 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/resources/js/openbis.js
@@ -1035,6 +1035,22 @@ openbis.prototype.listAttachmentsForSample = function(sampleId, allVersions, act
* ==========================================================================================
*/
+/**
+ * @see IGeneralInformationChangingService.registerSamples(String, String, String, String)
+ * @method
+ */
+openbis.prototype.registerSamples = function(sampleTypeCode, sessionKey, defaultGroupIdentifier, action) {
+ this._internal.ajaxRequest({
+ url: this._internal.generalInfoChangingServiceUrl,
+ data: { "method" : "registerSamples",
+ "params" : [ this.getSession(),
+ sampleTypeCode,
+ sessionKey,
+ defaultGroupIdentifier] },
+ success: action
+ });
+}
+
/**
* @see IGeneralInformationChangingService.updateSampleProperties(String, long, Map<String,String>)
* @method
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
index c626ee7847329b5ef04526414a36f5b262b01970..255360a46b0751fda896370c4f3d02262f3d914d 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
@@ -138,4 +138,17 @@ public interface IGeneralInformationChangingService extends IRpcService
public void removeFromMetaproject(String sessionToken, IMetaprojectId metaprojectId,
MetaprojectAssignmentsIds assignmentsToRemove);
+ /**
+ * Registers samples parsing a file stored on the HTTP Session.
+ *
+ * @param sampleTypeCode Sample type to parse
+ * @param sessionKey key of the file stored on the HTTP Session
+ * @param defaultGroupIdentifier key of the file stored on the HTTP Session
+ * @since 1.4
+ */
+ public boolean registerSamples(
+ final String sessionToken,
+ final String sampleTypeCode,
+ final String sessionKey,
+ final String defaultGroupIdentifier);
}