From 755fb78ee21b21e9d45a8f6d281b718cfaf7c4a6 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 26 Oct 2010 14:24:42 +0000
Subject: [PATCH] SE-308, SE-311 new methods added to ISampleLister
SVN: 18447
---
.../bo/samplelister/ISampleLister.java | 23 +++++
.../bo/samplelister/ISampleListingQuery.java | 6 ++
.../bo/samplelister/SampleLister.java | 50 +++++++++++
.../bo/samplelister/SampleListingWorker.java | 4 +-
.../dto/SampleRelationShipSkeleton.java | 61 +++++++++++++
.../generic/shared/dto/SampleSkeleton.java | 86 +++++++++++++++++++
6 files changed, 228 insertions(+), 2 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationShipSkeleton.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleLister.java
index 4741b115586..ea822fab056 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleLister.java
@@ -18,8 +18,11 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
import java.util.List;
+import ch.systemsx.cisd.common.collections.IValidator;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationShipSkeleton;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleSkeleton;
/**
* A role for fast sample listing.
@@ -33,5 +36,25 @@ public interface ISampleLister
* Returns a sorted list of {@link Sample}s that match given criteria.
*/
public List<Sample> list(ListOrSearchSampleCriteria criteria);
+
+ /**
+ * Returns the id of the relationship type of specified code. If code starts with an '$'
+ * it is interpreted as an internally defined relationship type.
+ *
+ * @throws IllegalArgumentException if code not known.
+ */
+ public long getRelationshipTypeID(String code);
+
+ /**
+ * Returns all samples as skeletons (thats is, only primary and foreign keys) fulfilling
+ * specified criteria.
+ */
+ public List<SampleSkeleton> listSampleBy(IValidator<SampleSkeleton> criteria);
+
+ /**
+ * Returns all sample relation ships as skeletons (thats is, only primary and foreign keys) fulfilling
+ * specified criteria.
+ */
+ public List<SampleRelationShipSkeleton> listSampleRelationShipsBy(IValidator<SampleRelationShipSkeleton> criteria);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index ca7fb9bfb49..3f625f05871 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -102,6 +102,12 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
{ TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRelationRecord> getParentRelations(long relationshipId,
LongSet childrenSampleIds);
+
+ @Select(sql = "select id, saty_id, grou_id, dbin_id, expe_id from samples", fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getSampleSkeletons();
+
+ @Select(sql = "select * from sample_relationships", fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRelationRecord> getSampleRelationshipSkeletons();
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
index 9b63edc9953..73a17efe293 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
@@ -16,12 +16,18 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
+import java.util.ArrayList;
import java.util.List;
+import net.lemnik.eodsql.DataIterator;
+
+import ch.systemsx.cisd.common.collections.IValidator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationShipSkeleton;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleSkeleton;
/**
* A business object for providing lists of samples (more precisely sets of samples) for the purpose
@@ -58,4 +64,48 @@ public class SampleLister implements ISampleLister
return SampleListingWorker.create(criteria, baseIndexURL, dao, referencedEntityDAO).load();
}
+ public long getRelationshipTypeID(String code)
+ {
+ return SampleListingWorker.getRelationId(dao.getQuery(), code);
+ }
+
+ public List<SampleSkeleton> listSampleBy(IValidator<SampleSkeleton> criteria)
+ {
+ DataIterator<SampleRecord> sampleSkeletons = dao.getQuery().getSampleSkeletons();
+ List<SampleSkeleton> result = new ArrayList<SampleSkeleton>();
+ for (SampleRecord sampleRecord : sampleSkeletons)
+ {
+ SampleSkeleton sampleSkeleton = new SampleSkeleton();
+ sampleSkeleton.setId(sampleRecord.id);
+ sampleSkeleton.setExperimentID(sampleRecord.expe_id);
+ sampleSkeleton.setSpaceID(sampleRecord.grou_id);
+ sampleSkeleton.setTypeID(sampleRecord.saty_id);
+ sampleSkeleton.setDatabaseInstanceID(sampleRecord.dbin_id);
+ if (criteria.isValid(sampleSkeleton))
+ {
+ result.add(sampleSkeleton);
+ }
+ }
+ return result;
+ }
+
+ public List<SampleRelationShipSkeleton> listSampleRelationShipsBy(
+ IValidator<SampleRelationShipSkeleton> criteria)
+ {
+ DataIterator<SampleRelationRecord> records = dao.getQuery().getSampleRelationshipSkeletons();
+ List<SampleRelationShipSkeleton> result = new ArrayList<SampleRelationShipSkeleton>();
+ for (SampleRelationRecord record : records)
+ {
+ SampleRelationShipSkeleton skeleton = new SampleRelationShipSkeleton();
+ skeleton.setRelationShipTypeID(record.relationship_id);
+ skeleton.setParentSampleID(record.sample_id_parent);
+ skeleton.setChildSampleID(record.sample_id_child);
+ if (criteria.isValid(skeleton))
+ {
+ result.add(skeleton);
+ }
+ }
+ return result;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
index 8cbddd6bdb7..ca6ea1523fe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
@@ -198,10 +198,10 @@ final class SampleListingWorker extends AbstractLister
this.enrichDependentSamples = criteria.isEnrichDependentSamplesWithProperties();
this.referencedEntityDAO = referencedEntityDAO;
this.parentRelationhipTypeId =
- getRelationId(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
+ getRelationId(query, BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
}
- private long getRelationId(String fullRelationCode)
+ static long getRelationId(ISampleListingQuery query, String fullRelationCode)
{
return query.getRelationshipTypeId(CodeConverter.tryToDatabase(fullRelationCode),
CodeConverter.isInternalNamespace(fullRelationCode));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationShipSkeleton.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationShipSkeleton.java
new file mode 100644
index 00000000000..89826b7026f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationShipSkeleton.java
@@ -0,0 +1,61 @@
+/*
+ * 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;
+
+/**
+ * Only primary and foreign keys of a sample relationship in the database.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SampleRelationShipSkeleton
+{
+ private long parentSampleID;
+
+ private long childSampleID;
+
+ private long relationShipTypeID;
+
+ public final long getParentSampleID()
+ {
+ return parentSampleID;
+ }
+
+ public final void setParentSampleID(long parentSampleID)
+ {
+ this.parentSampleID = parentSampleID;
+ }
+
+ public final long getChildSampleID()
+ {
+ return childSampleID;
+ }
+
+ public final void setChildSampleID(long childSampleID)
+ {
+ this.childSampleID = childSampleID;
+ }
+
+ public final long getRelationShipTypeID()
+ {
+ return relationShipTypeID;
+ }
+
+ public final void setRelationShipTypeID(long relationShipTypeID)
+ {
+ this.relationShipTypeID = relationShipTypeID;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
new file mode 100644
index 00000000000..79265eac888
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleSkeleton.java
@@ -0,0 +1,86 @@
+/*
+ * 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;
+
+/**
+ * Only primary and foreign keys of a sample in the database.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SampleSkeleton
+{
+ private long id;
+
+ private Long databaseInstanceID;
+
+ private Long spaceID;
+
+ private long typeID;
+
+ private Long experimentID;
+
+ public final long getId()
+ {
+ return id;
+ }
+
+ public final void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public final Long getDatabaseInstanceID()
+ {
+ return databaseInstanceID;
+ }
+
+ public final void setDatabaseInstanceID(Long databaseInstanceID)
+ {
+ this.databaseInstanceID = databaseInstanceID;
+ }
+
+ public final Long getSpaceID()
+ {
+ return spaceID;
+ }
+
+ public final void setSpaceID(Long spaceID)
+ {
+ this.spaceID = spaceID;
+ }
+
+ public final long getTypeID()
+ {
+ return typeID;
+ }
+
+ public final void setTypeID(long typeID)
+ {
+ this.typeID = typeID;
+ }
+
+ public final Long getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(Long experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+}
--
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