From b21ab898f7f370d7df877f06a6985f1ccea4d3d5 Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Wed, 2 Jun 2010 07:26:26 +0000
Subject: [PATCH] [LMS-1529] create wells on the fly when datasets are
registered before the library is registered; allow to "update" already
existing samples on "Library" registration
SVN: 16251
---
.../ch/systemsx/cisd/bds/hcs/Location.java | 13 +++
.../systemsx/cisd/bds/hcs/LocationTest.java | 21 ++++
.../cisd/common/geometry/ConversionUtils.java | 15 +++
.../server/EncapsulatedOpenBISService.java | 9 ++
.../shared/IEncapsulatedOpenBISService.java | 7 ++
.../openbis/generic/server/ETLService.java | 93 +++++++++++++++
.../generic/server/ETLServiceLogger.java | 12 ++
.../authorization/PredicateExecutor.java | 6 +
.../generic/shared/IETLLIMSService.java | 16 +++
.../IAuthorizationDataProvider.java | 6 +
.../SampleComponentsDescriptionPredicate.java | 51 ++++++++
.../predicate/SamplePermIdPredicate.java | 74 ++++++++++++
.../openbis/generic/shared/basic/PermId.java | 94 +++++++++++++++
.../shared/basic/dto/NewSamplesWithTypes.java | 12 ++
.../dto/SampleComponentsDescription.java | 73 ++++++++++++
.../server/GenericBusinessObjectFactory.java | 7 ++
.../plugin/generic/server/GenericServer.java | 55 ++++++++-
.../generic/server/GenericServerLogger.java | 15 +++
.../server/IGenericBusinessObjectFactory.java | 3 +
.../server/SampleRegisterOrUpdateUtil.java | 110 ++++++++++++++++++
.../plugin/generic/shared/IGenericServer.java | 11 ++
.../shared/IETLLIMSService.java.expected | 16 +++
.../shared/IGenericServer.java.expected | 11 ++
.../openbis/dss/etl/HCSDatasetUploader.java | 61 +++++++---
.../dss/etl/dataaccess/IImagingUploadDAO.java | 4 +-
.../dss/etl/dataaccess/ImgSpotDTO.java | 16 ++-
.../client/web/server/LibraryExtractor.java | 12 +-
.../web/server/LibraryRegistrationTask.java | 2 +-
.../shared/basic/dto/ScreeningConstants.java | 4 +
.../source/sql/postgresql/001/schema-001.sql | 2 +
.../etl/dataaccess/ImagingUploadDAOTest.java | 3 +
31 files changed, 814 insertions(+), 20 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleComponentsDescriptionPredicate.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SamplePermIdPredicate.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermId.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleComponentsDescription.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
diff --git a/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
index 9641a1729c2..6f7ad4509e0 100644
--- a/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
+++ b/bds/source/java/ch/systemsx/cisd/bds/hcs/Location.java
@@ -92,6 +92,19 @@ public final class Location
}
}
+ /**
+ * For given location returns corresponding matrix coordinate.
+ */
+ public static final String tryCreateMatrixCoordinateFromLocation(final Location location)
+ {
+ if (location == null)
+ {
+ throw new IllegalArgumentException("Location unspecified");
+ }
+ Point point = new Point(location.getY() - 1, location.getX() - 1);
+ return ConversionUtils.convertToSpreadsheetLocation(point);
+ }
+
//
// Object
//
diff --git a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/LocationTest.java b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/LocationTest.java
index 7e3cb097282..8b072e1054c 100644
--- a/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/LocationTest.java
+++ b/bds/sourceTest/java/ch/systemsx/cisd/bds/hcs/LocationTest.java
@@ -101,4 +101,25 @@ public final class LocationTest
assertEquals(new Location(7, 26), Location.tryCreateLocationFromMatrixCoordinate("z7"));
assertEquals(new Location(34, 15), Location.tryCreateLocationFromMatrixCoordinate("O34"));
}
+
+ @Test
+ public final void testCreateMatrixCoordinateFromLocation()
+ {
+ assertEquals("A1", Location.tryCreateMatrixCoordinateFromLocation(new Location(1, 1)));
+ assertEquals("A2", Location.tryCreateMatrixCoordinateFromLocation(new Location(2, 1)));
+ assertEquals("Z7", Location.tryCreateMatrixCoordinateFromLocation(new Location(7, 26)));
+ assertEquals("O34", Location.tryCreateMatrixCoordinateFromLocation(new Location(34, 15)));
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public final void testCreateMatrixCoordinateFromTooBigNumber()
+ {
+ Location.tryCreateMatrixCoordinateFromLocation(new Location(134, 27));
+ }
+
+ @Test(expectedExceptions = IllegalArgumentException.class)
+ public final void testCreateMatrixCoordinateFromNullLocation()
+ {
+ Location.tryCreateMatrixCoordinateFromLocation(null);
+ }
}
diff --git a/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java b/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
index 3c0d8e92b43..a07404e2d33 100644
--- a/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
@@ -90,6 +90,21 @@ public class ConversionUtils
}
+ static public String convertToSpreadsheetLocation(Point p)
+ {
+ if (p == null)
+ {
+ throw new IllegalArgumentException("Unspecified point.");
+ }
+ if (p.getX() >= 26 || p.getX() < 0)
+ {
+ throw new IllegalArgumentException("Unsupported value: " + p.getX());
+ }
+ char x = (char) (p.getX() + 'A');
+ int y = p.getY() + 1;
+ return String.format("%s%s", x, y);
+ }
+
private static int getLetterNumber(final char ch)
{
return Character.toUpperCase(ch) - 'A' + 1;
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 50f357308a1..b4df1ab81f4 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
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.FactoryBean;
@@ -52,6 +54,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
@@ -697,4 +700,10 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
{
service.unarchiveDatasets(sessionToken, dataSetCodes);
}
+
+ public Map<String, String> listOrRegisterComponents(String containerPermId, Set<String> codes,
+ String sampleTypeCode) throws UserFailureException
+ {
+ return service.listOrRegisterComponents(sessionToken, new SampleComponentsDescription(containerPermId, codes, sampleTypeCode));
+ }
}
\ 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 0d87d03d0c0..aefe20cecb5 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
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.dss.generic.shared;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -38,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -223,4 +226,8 @@ public interface IEncapsulatedOpenBISService
/** See {@link IETLLIMSService#checkSpaceAccess(String, SpaceIdentifier)} */
public void checkSpaceAccess(String sToken, SpaceIdentifier spaceId);
+
+ /** See {@link IETLLIMSService#listOrRegisterComponents(String, SampleComponentsDescription)} */
+ public Map<String, String> listOrRegisterComponents(final String containerPermId,
+ Set<String> codes, String sampleTypeCode) throws UserFailureException;
}
\ No newline at end of file
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 e0a4d496a16..4dfbea3e51e 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
@@ -18,10 +18,12 @@ package ch.systemsx.cisd.openbis.generic.server;
import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_WEB_APPLICATION_NAME;
+import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import ch.systemsx.cisd.authentication.IAuthenticationService;
@@ -84,6 +86,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
@@ -705,4 +708,94 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return url;
}
+
+ public Map<String, String> listOrRegisterComponents(String sessionToken,
+ SampleComponentsDescription components) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert components != null : "Unspecified components.";
+
+ final Session session = getSession(sessionToken);
+ SamplePE container = getContainer(components.getContainerPermId());
+ Set<String> codesToGet = new HashSet<String>(components.getCodes());
+ Map<String, String> result = new HashMap<String, String>();
+ tryLoadSamples(session, listSamplesForContainer(session, container), codesToGet, result);
+ if (codesToGet.size() > 0)
+ {
+ registerSamples(components.getSampleTypeCode(), session, container, codesToGet);
+ tryLoadSamples(session, listSamplesForContainer(session, container), codesToGet, result);
+ }
+ assert codesToGet.size() == 0 : "All samples should exist at this point";
+ return result;
+ }
+
+ private void registerSamples(String sampleTypeCode, final Session session, SamplePE container,
+ Set<String> codesToGet)
+ {
+ final SampleTypePE sampleTypePE = getSampleType(sampleTypeCode);
+ List<NewSample> newSamples = new ArrayList<NewSample>();
+ for (String code : codesToGet)
+ {
+ String groupPrefix =
+ container.getGroup() != null ? ("/" + container.getGroup().getCode() + "/")
+ : "/";
+ newSamples.add(new NewSample(groupPrefix + code, SampleTypeTranslator.translate(
+ sampleTypePE, null), null, container.getIdentifier()));
+ }
+ getSampleTypeSlaveServerPlugin(sampleTypePE).registerSamples(session, newSamples);
+ }
+
+ private SamplePE getContainer(String containerPermId)
+ {
+ SamplePE container = daoFactory.getSampleDAO().tryToFindByPermID(containerPermId);
+ if (container == null)
+ {
+ throw new UserFailureException(String.format("Container '%s' not found.",
+ containerPermId));
+ }
+ return container;
+ }
+
+ List<Sample> listSamplesForContainer(Session session, SamplePE container)
+ {
+ ListOrSearchSampleCriteria criteria = createListSamplesByContainerCriteria(container);
+ return businessObjectFactory.createSampleLister(session).list(criteria);
+ }
+
+ private SampleTypePE getSampleType(String sampleTypeCode)
+ {
+ final SampleTypePE sampleTypePE =
+ getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
+ if (sampleTypePE == null)
+ {
+ throw UserFailureException.fromTemplate("Sample type with code '%s' does not exist.",
+ sampleTypeCode);
+ }
+ return sampleTypePE;
+ }
+
+ private static ListOrSearchSampleCriteria createListSamplesByContainerCriteria(
+ SamplePE container)
+ {
+ ListOrSearchSampleCriteria criteria =
+ new ListOrSearchSampleCriteria(ListOrSearchSampleCriteria
+ .createForContainer(new TechId(container.getId())));
+ criteria.setEnrichDependentSamplesWithProperties(false);
+ return criteria;
+ }
+
+ private static void tryLoadSamples(final Session session, List<Sample> samples,
+ Set<String> codesToGet, Map<String, String> result)
+ {
+ for (Sample s : samples)
+ {
+ String subCode = s.getSubCode();
+ if (codesToGet.contains(subCode))
+ {
+ result.put(subCode, s.getPermId());
+ codesToGet.remove(subCode);
+ }
+ }
+ }
+
}
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 1392463bf4f..35b409bb47c 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server;
import java.util.List;
+import java.util.Map;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -41,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DatastoreServiceDescriptions;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -276,4 +278,14 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
logAccess(sessionToken, "getDefaultDataStoreBaseURL");
return null;
}
+
+ public Map<String, String> listOrRegisterComponents(String sessionToken,
+ SampleComponentsDescription components)
+ throws UserFailureException
+ {
+ logTracking(sessionToken, "listOrRegisterComponents", "CONTAINER(%s) CODES(%s) TYPE(%s)",
+ components.getContainerPermId(), components.getCodes().size(), components.getSampleTypeCode());
+
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
index 32a166434b6..e14b13d96a0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ShouldFl
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ArrayPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.CollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.IPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.basic.PermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetAccessPE;
@@ -331,6 +332,11 @@ public final class PredicateExecutor
return daoFactory.getSampleDAO().getByTechId(techId);
}
+ public SamplePE getSample(PermId id)
+ {
+ return daoFactory.getSampleDAO().tryToFindByPermID(id.getId());
+ }
+
public GridCustomFilterPE getGridCustomFilter(TechId techId)
{
return daoFactory.getGridCustomFilterDAO().getByTechId(techId);
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 46d3c841541..32900ffa715 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared;
import java.util.List;
+import java.util.Map;
import org.springframework.transaction.annotation.Transactional;
@@ -32,6 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampl
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.SampleComponentsDescriptionPredicate;
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;
@@ -58,6 +60,7 @@ 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;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -407,4 +410,17 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleSet.USER)
public void checkSpaceAccess(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) SpaceIdentifier spaceId);
+
+ /**
+ * Load perm ids of samples contained in given container. Register samples that don't exist.
+ *
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.ETL_SERVER)
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
+ public Map<String, String> listOrRegisterComponents(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleComponentsDescriptionPredicate.class) SampleComponentsDescription components)
+ throws UserFailureException;
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
index c7e3fb51d84..66de4b37e1b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.authorization;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.IDatabaseInstanceFinder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.PermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetAccessPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GridCustomColumnPE;
@@ -69,6 +70,11 @@ public interface IAuthorizationDataProvider extends IDatabaseInstanceFinder
*/
public SamplePE getSample(TechId techId);
+ /**
+ * Returns the sample with given <var>permId</var>.
+ */
+ public SamplePE getSample(PermId id);
+
/**
* Returns the filter with given <var>techId</var>
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleComponentsDescriptionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleComponentsDescriptionPredicate.java
new file mode 100644
index 00000000000..1ff04eab3a6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleComponentsDescriptionPredicate.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright 2008 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.authorization.predicate;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.PermId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
+
+/**
+ * An <code>IPredicate</code> implementation for {@link SampleComponentsDescription}.
+ *
+ * @author Izabela Adamczyk
+ */
+public final class SampleComponentsDescriptionPredicate extends
+ DelegatedPredicate<PermId, SampleComponentsDescription>
+{
+ public SampleComponentsDescriptionPredicate()
+ {
+ super(new SamplePermIdPredicate());
+ }
+
+ //
+ // DelegatedPredicate
+ //
+
+ @Override
+ public final PermId convert(final SampleComponentsDescription value)
+ {
+ return new PermId(value.getContainerPermId());
+ }
+
+ @Override
+ public final String getCandidateDescription()
+ {
+ return "new sample";
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SamplePermIdPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SamplePermIdPredicate.java
new file mode 100644
index 00000000000..4a9a0214a8d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SamplePermIdPredicate.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2009 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.authorization.predicate;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.IAuthorizationDataProvider;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.RoleWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.PermId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * An <code>IPredicate</code> implementation based on permId of a sample.
+ *
+ * @author Izabela Adamczyk
+ */
+public class SamplePermIdPredicate extends AbstractDatabaseInstancePredicate<PermId>
+{
+
+ private final SampleOwnerIdentifierPredicate sampleOwnerIdentifierPredicate;
+
+ public SamplePermIdPredicate()
+ {
+ this(true);
+ }
+
+ public SamplePermIdPredicate(boolean isReadAccess)
+ {
+ sampleOwnerIdentifierPredicate = new SampleOwnerIdentifierPredicate(isReadAccess);
+ }
+
+ //
+ // AbstractPredicate
+ //
+
+ @Override
+ public final void init(IAuthorizationDataProvider provider)
+ {
+ super.init(provider);
+ sampleOwnerIdentifierPredicate.init(provider);
+ }
+
+ @Override
+ public final String getCandidateDescription()
+ {
+ return "sample perm id";
+ }
+
+ @Override
+ final Status doEvaluation(final PersonPE person, final List<RoleWithIdentifier> allowedRoles,
+ final PermId id)
+ {
+ SamplePE sample = authorizationDataProvider.getSample(id);
+ return sampleOwnerIdentifierPredicate.doEvaluation(person, allowedRoles, sample
+ .getSampleIdentifier());
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermId.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermId.java
new file mode 100644
index 00000000000..ee8a21427f4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/PermId.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2009 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.basic;
+
+import java.io.Serializable;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * Perm id of an entity.
+ *
+ * @author Izabela Adamczyk
+ */
+public class PermId implements IsSerializable, Serializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private String id;
+
+ protected PermId()
+ {
+ // for serialization
+ }
+
+ public PermId(String id)
+ {
+ assert id != null : "id cannot be null";
+ this.id = id;
+ }
+
+ public String getId()
+ {
+ return id;
+ }
+
+ public void setId(String id)
+ {
+ this.id = id;
+ }
+
+ public static PermId create(IPermIdHolder holder)
+ {
+ if (holder == null || holder.getPermId() == null)
+ {
+ return null;
+ } else
+ {
+ return new PermId(holder.getPermId());
+ }
+ }
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof PermId == false)
+ {
+ return false;
+ }
+ return this.toString().equals(obj.toString());
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return this.toString().hashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return id;
+ }
+
+}
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 4215e1ea27e..3c472c69c5e 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
@@ -29,6 +29,18 @@ public class NewSamplesWithTypes
List<NewSample> newSamples;
+ boolean allowUpdateIfExist = false;
+
+ public boolean isAllowUpdateIfExist()
+ {
+ return allowUpdateIfExist;
+ }
+
+ public void setAllowUpdateIfExist(boolean allowUpdateIfExist)
+ {
+ this.allowUpdateIfExist = allowUpdateIfExist;
+ }
+
public NewSamplesWithTypes()
{
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleComponentsDescription.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleComponentsDescription.java
new file mode 100644
index 00000000000..2a62309b960
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleComponentsDescription.java
@@ -0,0 +1,73 @@
+/*
+ * 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.dto;
+
+import java.io.Serializable;
+import java.util.Set;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+
+/**
+ * Stores basic information about sample components.
+ *
+ * @author Izabela Adamczyk
+ */
+public class SampleComponentsDescription implements IsSerializable, Serializable
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private final String containerPermId;
+
+ private Set<String> codes;
+
+ private String sampleTypeCode;
+
+ public SampleComponentsDescription(String containerPermId, Set<String> codes,
+ String sampleTypeCode)
+ {
+ this.containerPermId = containerPermId;
+ this.codes = codes;
+ this.sampleTypeCode = sampleTypeCode;
+ }
+
+ public String getContainerPermId()
+ {
+ return containerPermId;
+ }
+
+ public Set<String> getCodes()
+ {
+ return codes;
+ }
+
+ public void setCodes(Set<String> codes)
+ {
+ this.codes = codes;
+ }
+
+ public String getSampleTypeCode()
+ {
+ return sampleTypeCode;
+ }
+
+ public void setSampleTypeCode(String sampleTypeCode)
+ {
+ this.sampleTypeCode = sampleTypeCode;
+ }
+}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
index a3c7049fd9c..b80b50c230f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
@@ -26,6 +26,8 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.SampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.AbstractPluginBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames;
@@ -83,4 +85,9 @@ public final class GenericBusinessObjectFactory extends AbstractPluginBusinessOb
{
return getCommonBusinessObjectFactory().createProjectBO(session);
}
+
+ public ISampleLister createSampleLister(Session session)
+ {
+ return SampleLister.create(getDaoFactory(), session.getBaseIndexURL());
+ }
}
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 dd938ccd1c9..1edcea074df 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
@@ -24,6 +24,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import javax.annotation.Resource;
@@ -63,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
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.SampleBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -253,6 +255,38 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
filename, version));
}
+ public final void registerOrUpdateSamples(final String sessionToken,
+ final List<NewSamplesWithTypes> newSamplesWithType) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ final Session session = getSession(sessionToken);
+ for (NewSamplesWithTypes samples : newSamplesWithType)
+ {
+ if (samples.isAllowUpdateIfExist() == false)
+ {
+ registerSamples(session, samples);
+ } else
+ {
+ registerOrUpdate(session, samples);
+ }
+ }
+ }
+
+ private void registerOrUpdate(final Session session, NewSamplesWithTypes samples)
+ {
+ List<Sample> existingSamples =
+ businessObjectFactory.createSampleLister(session).list(
+ SampleRegisterOrUpdateUtil.createListSamplesByCodeCriteria(samples
+ .getNewSamples()));
+ List<NewSample> samplesToUpdate =
+ SampleRegisterOrUpdateUtil.getSamplesToUpdate(samples, existingSamples);
+ List<NewSample> samplesToRegister = new ArrayList<NewSample>(samples.getNewSamples());
+ samplesToRegister.removeAll(samplesToUpdate);
+ registerSamples(session,
+ new NewSamplesWithTypes(samples.getSampleType(), samplesToRegister));
+ updateSamples(session, new NewSamplesWithTypes(samples.getSampleType(), samplesToUpdate));
+ }
+
public final void registerSamples(final String sessionToken,
final List<NewSamplesWithTypes> newSamplesWithType) throws UserFailureException
{
@@ -368,7 +402,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
final String parentIdentifierOrNull = updatedSample.getParentIdentifier();
final String containerIdentifierOrNull = updatedSample.getContainerIdentifier();
final SampleBatchUpdateDetails batchUpdateDetails =
- ((UpdatedSample) updatedSample).getBatchUpdateDetails();
+ createBatchUpdateDetails(updatedSample);
batchUpdateSample(session, new SampleBatchUpdatesDTO(oldSampleIdentifier, properties,
experimentIdentifierOrNull, newSampleIdentifier, parentIdentifierOrNull,
@@ -376,6 +410,25 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
}
}
+ SampleBatchUpdateDetails createBatchUpdateDetails(NewSample sample)
+ {
+ if (sample instanceof UpdatedSample)
+ {
+ return ((UpdatedSample) sample).getBatchUpdateDetails();
+ } else
+ {
+ IEntityProperty[] properties = sample.getProperties();
+ Set<String> propertyCodes = new HashSet<String>();
+ for (IEntityProperty p : properties)
+ {
+ propertyCodes.add(p.getPropertyType().getCode());
+ }
+ SampleBatchUpdateDetails result =
+ new SampleBatchUpdateDetails(false, false, false, propertyCodes);
+ return result;
+ }
+ }
+
public void registerExperiment(String sessionToken, NewExperiment newExperiment,
final Collection<NewAttachment> attachments)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
index de1ea77f53b..53df577d8cd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerLogger.java
@@ -233,4 +233,19 @@ final class GenericServerLogger extends AbstractServerLogger implements IGeneric
materialTypeCode, materials.size());
}
+ public void registerOrUpdateSamples(String sessionToken,
+ List<NewSamplesWithTypes> newSamplesWithType) throws UserFailureException
+ {
+ StringBuilder sb = new StringBuilder();
+ for (NewSamplesWithTypes s : newSamplesWithType)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(s.getSampleType().getCode() + ":" + s.getNewSamples().size());
+ }
+ logTracking(sessionToken, "register_or_update_samples", sb.toString());
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
index 46d8ca1ec6e..9e7339c8765 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
@@ -72,4 +73,6 @@ public interface IGenericBusinessObjectFactory
* Creates a {@link IExternalDataTable} <i>Business Object</i>.
*/
public IExternalDataTable createExternalDataTable(final Session session);
+
+ public ISampleLister createSampleLister(Session session);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
new file mode 100644
index 00000000000..1a6748dd991
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/SampleRegisterOrUpdateUtil.java
@@ -0,0 +1,110 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.generic.server;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+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.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * Utility class for sample update or registration.
+ *
+ * @author Izabela Adamczyk
+ */
+public class SampleRegisterOrUpdateUtil
+{
+ private static final String INSTANCE_SEPARATOR = "/";
+
+ /**
+ * Returns a list of samples that already exist and should be updated.
+ */
+ static List<NewSample> getSamplesToUpdate(NewSamplesWithTypes samples,
+ List<Sample> existingSamples)
+ {
+ List<NewSample> samplesToUpdate = new ArrayList<NewSample>();
+ for (NewSample ns : samples.getNewSamples())
+ {
+ for (Sample es : existingSamples)
+ {
+ if (isMatching(ns.getIdentifier(), es.getIdentifier()))
+ {
+ samplesToUpdate.add(ns);
+ }
+ }
+ }
+ return samplesToUpdate;
+ }
+
+ /**
+ * Creates {@link ListOrSearchSampleCriteria} narrowing listing result to samples given codes.
+ */
+ static ListOrSearchSampleCriteria createListSamplesByCodeCriteria(List<NewSample> samples)
+ {
+ List<String> codes = new ArrayList<String>();
+ for (NewSample s : samples)
+ {
+ codes.add(extractCodeForSampleListingCriteria(s));
+ }
+ String[] codesAsArray = codes.toArray(new String[0]);
+ ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(codesAsArray);
+ return criteria;
+ }
+
+ /**
+ * Checks if given identifiers are matching (db instance is not considered).
+ */
+ private static boolean isMatching(String i1, String i2)
+ {
+ if (i1 != null && i2 != null)
+ {
+ return dropDatabaseInstance(i1).equals(dropDatabaseInstance(i2));
+ } else
+ {
+ return i1 == i2;
+ }
+ }
+
+ private static String dropDatabaseInstance(String id)
+ {
+ assert id != null;
+ assert id.contains(INSTANCE_SEPARATOR);
+ if (id.startsWith(INSTANCE_SEPARATOR))
+ {
+ return id;
+ } else
+ {
+ return id.substring(id.indexOf(INSTANCE_SEPARATOR));
+ }
+
+ }
+
+ private static String extractCodeForSampleListingCriteria(NewSample s)
+ {
+ SampleIdentifier parsedIdentifier = SampleIdentifierFactory.parse(s.getIdentifier());
+ String subcode = parsedIdentifier.getSampleSubCode();
+ String code = parsedIdentifier.getSampleCode();
+ return StringUtils.isBlank(subcode) ? code : subcode;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
index 1905503bc5b..8c04589f6a5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java
@@ -143,6 +143,17 @@ public interface IGenericServer extends IServer
@AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class) final List<NewSamplesWithTypes> newSamplesWithType)
throws UserFailureException;
+ /**
+ * Registers or updates samples of different types in batches.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
+ public void registerOrUpdateSamples(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class) final List<NewSamplesWithTypes> newSamplesWithType)
+ throws UserFailureException;
+
/**
* Updates samples of different types in batches.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index 46d3c841541..32900ffa715 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared;
import java.util.List;
+import java.util.Map;
import org.springframework.transaction.annotation.Transactional;
@@ -32,6 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampl
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.SampleComponentsDescriptionPredicate;
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;
@@ -58,6 +60,7 @@ 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;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleComponentsDescription;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -407,4 +410,17 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleSet.USER)
public void checkSpaceAccess(String sessionToken,
@AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) SpaceIdentifier spaceId);
+
+ /**
+ * Load perm ids of samples contained in given container. Register samples that don't exist.
+ *
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.ETL_SERVER)
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
+ public Map<String, String> listOrRegisterComponents(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = SampleComponentsDescriptionPredicate.class) SampleComponentsDescription components)
+ throws UserFailureException;
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
index 1905503bc5b..8c04589f6a5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/shared/IGenericServer.java.expected
@@ -143,6 +143,17 @@ public interface IGenericServer extends IServer
@AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class) final List<NewSamplesWithTypes> newSamplesWithType)
throws UserFailureException;
+ /**
+ * Registers or updates samples of different types in batches.
+ */
+ @Transactional
+ @RolesAllowed(RoleSet.USER)
+ @DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
+ public void registerOrUpdateSamples(
+ final String sessionToken,
+ @AuthorizationGuard(guardClass = NewSamplesWithTypePredicate.class) final List<NewSamplesWithTypes> newSamplesWithType)
+ throws UserFailureException;
+
/**
* Updates samples of different types in batches.
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index 6bb1120e837..48063b947ad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -18,11 +18,13 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.Map.Entry;
+import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
@@ -33,6 +35,9 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgSpotDTO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
* @author Tomasz Pylak
@@ -127,17 +132,17 @@ class HCSDatasetUploader
throw createInvalidNewChannelException(expId, existingChannels, channelName);
}
// a channel with a specified name already exists for an experiment, its description
- // will be updated
+ // will be updated
if (existingChannel.getWavelength().equals(channelDTO.getWavelength()) == false)
- {
+ {
throw UserFailureException.fromTemplate(
- "There are already datasets registered for the experiment "
- + "which use the same channel name, but with a different wavelength! "
+ "There are already datasets registered for the experiment "
+ + "which use the same channel name, but with a different wavelength! "
+ "Channel %s, old wavelength %d, new wavelength %d.", channelName,
existingChannel.getWavelength(), channelDTO.getWavelength());
- }
- channelDTO.setId(existingChannel.getId());
- dao.updateChannel(channelDTO);
+ }
+ channelDTO.setId(existingChannel.getId());
+ dao.updateChannel(channelDTO);
return channelDTO;
}
@@ -153,10 +158,10 @@ class HCSDatasetUploader
}
private ImgChannelDTO createChannel(long expId, HCSImageFileExtractionResult.Channel channel)
- {
+ {
ImgChannelDTO channelDTO = makeChannelDTO(channel, expId);
- long channelId = dao.addChannel(channelDTO);
- channelDTO.setId(channelId);
+ long channelId = dao.addChannel(channelDTO);
+ channelDTO.setId(channelId);
return channelDTO;
}
@@ -285,16 +290,17 @@ class HCSDatasetUploader
List<ImgSpotDTO> oldSpots = dao.listSpots(contId);
List<ImgSpotDTO> newSpots =
createNewSpots(contId, images, oldSpots, info.getContainerRows(), info
- .getContainerColumns());
+ .getContainerColumns(), info.getContainerPermId());
newSpots.addAll(oldSpots);
return makeTechIdMatrix(newSpots, info.getContainerRows(), info.getContainerColumns());
}
private List<ImgSpotDTO> createNewSpots(long contId, List<AcquiredPlateImage> images,
- List<ImgSpotDTO> existingSpots, int rows, int columns)
+ List<ImgSpotDTO> existingSpots, int rows, int columns, String containerPermId)
{
Boolean[][] newSpotMatrix = extractNewSpots(rows, columns, images, existingSpots);
List<ImgSpotDTO> newSpots = makeSpotDTOs(newSpotMatrix, contId);
+ enrichWithPermIds(newSpots, containerPermId);
for (ImgSpotDTO spot : newSpots)
{
long id = dao.addSpot(spot);
@@ -303,8 +309,35 @@ class HCSDatasetUploader
return newSpots;
}
- private static Boolean[][] extractNewSpots(int rows, int columns,
- List<AcquiredPlateImage> images, List<ImgSpotDTO> existingSpots)
+ private void enrichWithPermIds(List<ImgSpotDTO> newSpots, String containerPermId)
+ {
+ Map<String, String> permIds = getOrCreateWells(newSpots, containerPermId);
+ for (ImgSpotDTO spot : newSpots)
+ {
+ spot.setPermId(permIds.get(createCoordinate(spot)));
+ }
+ }
+
+ private Map<String, String> getOrCreateWells(List<ImgSpotDTO> newSpots, String containerPermId)
+ {
+ IEncapsulatedOpenBISService server = ServiceProvider.getOpenBISService();
+ Set<String> codes = new HashSet<String>();
+ for (ImgSpotDTO spot : newSpots)
+ {
+ codes.add(createCoordinate(spot));
+ }
+ return server.listOrRegisterComponents(containerPermId, codes,
+ ScreeningConstants.OLIGO_WELL_TYPE_CODE);
+ }
+
+ String createCoordinate(ImgSpotDTO spot)
+ {
+ return Location.tryCreateMatrixCoordinateFromLocation(new Location(spot.getColumn(), spot
+ .getRow()));
+ }
+
+ private static Boolean[][] extractNewSpots(int rows, int columns, List<AcquiredPlateImage> images,
+ List<ImgSpotDTO> existingSpots)
{
Boolean[][] spots = extractExistingSpots(rows, columns, images);
unmarkSpots(existingSpots, spots);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
index 54ece75b656..430795bf0d6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
@@ -103,8 +103,8 @@ public interface IImagingUploadDAO extends TransactionQuery
+ "(?{1.filePath}, ?{1.page}, ?{1.colorComponentAsString}) returning ID")
public long addImage(ImgImageDTO image);
- @Select("insert into SPOTS (X, Y, CONT_ID) values "
- + "(?{1.column}, ?{1.row}, ?{1.containerId}) returning ID")
+ @Select("insert into SPOTS (X, Y, CONT_ID, PERM_ID) values "
+ + "(?{1.column}, ?{1.row}, ?{1.containerId}, ?{1.permId}) returning ID")
public long addSpot(ImgSpotDTO spot);
// updates
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
index 8815546b8ab..2927d99d3ca 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
@@ -29,6 +29,9 @@ public class ImgSpotDTO extends AbstractHashable
@AutoGeneratedKeys
private long id;
+ @ResultColumn("PERM_ID")
+ private String permId;
+
// position in the container, one-based (e.g. well column)
@ResultColumn("X")
private Integer column;
@@ -46,13 +49,24 @@ public class ImgSpotDTO extends AbstractHashable
// All Data-Object classes must have a default constructor.
}
- public ImgSpotDTO(Integer row, Integer column, long containerId)
+ public ImgSpotDTO(/* String permId, */Integer row, Integer column, long containerId)
{
+ /* this.permId = permId; */
this.column = column;
this.row = row;
this.containerId = containerId;
}
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
public long getId()
{
return id;
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 1904fc6cc4f..bed76500635 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
@@ -108,7 +108,17 @@ class LibraryExtractor
.asList(new NamedInputStream(new FileInputStream(platesFile), platesFile
.getName(), null)), null, null, true,
BatchOperationKind.REGISTRATION);
- return prepared.getSamples();
+ List<NewSamplesWithTypes> samples = prepared.getSamples();
+ setUpdatableTypes(samples);
+ return samples;
+ }
+
+ private static void setUpdatableTypes(List<NewSamplesWithTypes> samples)
+ {
+ for (NewSamplesWithTypes s : samples)
+ {
+ s.setAllowUpdateIfExist(true);
+ }
}
private static List<NewMaterial> extractMaterials(File genesFile) throws FileNotFoundException
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
index 98492ed33d6..fe67c6484c5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryRegistrationTask.java
@@ -90,7 +90,7 @@ class LibraryRegistrationTask implements Runnable
}
try
{
- genericServer.registerSamples(sessionToken, newSamplesWithType);
+ genericServer.registerOrUpdateSamples(sessionToken, newSamplesWithType);
for (NewSamplesWithTypes s : newSamplesWithType)
{
message.append("Successfuly registered " + s.getNewSamples().size()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index 40d8d451d4f..66969a8398f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -50,6 +50,10 @@ public class ScreeningConstants
// type of the dataset which stores image analysis data, there should be at most one
public static final String IMAGE_ANALYSIS_DATASET_TYPE = "HCS_IMAGE_ANALYSIS_DATA";
+ public static final String OLIGO_WELL_TYPE_CODE = "OLIGO_WELL";
+
+ public static final String CONTROL_WELL_TYPE_CODE = "CONTROL_WELL";
+
public static final String PLATE_PLUGIN_TYPE_CODE = "PLATE";
public static final String LIBRARY_PLUGIN_TYPE_CODE = "LIBRARY";
diff --git a/screening/source/sql/postgresql/001/schema-001.sql b/screening/source/sql/postgresql/001/schema-001.sql
index 5385d12e09b..ddd0cc8dd89 100644
--- a/screening/source/sql/postgresql/001/schema-001.sql
+++ b/screening/source/sql/postgresql/001/schema-001.sql
@@ -45,6 +45,7 @@ CREATE INDEX CONTAINERS_EXPE_IDX ON CONTAINERS(EXPE_ID);
CREATE TABLE SPOTS (
ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
-- position in the container, one-based
X INTEGER,
@@ -52,6 +53,7 @@ CREATE TABLE SPOTS (
CONT_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
CONSTRAINT FK_SPOT_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
index 9f7992d56c9..a8eb51dcc7f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
@@ -39,6 +39,8 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO.ColorComponent;
public class ImagingUploadDAOTest extends AbstractDBTest
{
+ private static final String PERM_ID = "PERM_ID";
+
private static final int PAGE = 1;
private static final int Y_TILE_ROW = 2;
@@ -202,6 +204,7 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private long addSpot(long containerId)
{
final ImgSpotDTO spot = new ImgSpotDTO(Y_WELL_ROW, X_WELL_COLUMN, containerId);
+ spot.setPermId(PERM_ID);
return dao.addSpot(spot);
}
--
GitLab