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/** |
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$Id$ |
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Copyright (C) 2015 Nicklas Nordborg |
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.util.listable; |
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import java.util.HashSet; |
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import java.util.Set; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.DerivedBioAssay; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemQuery; |
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import net.sf.basedb.core.query.Expressions; |
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import net.sf.basedb.core.query.Hql; |
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import net.sf.basedb.core.query.Restrictions; |
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/** |
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Source item transformer implementation that transform physical bioassay items |
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to derived bioassays. This implementation transform to all derived bioassays |
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that are descendants of the physical bioassays and may optionally limit the |
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derived bioassays that are related to parent collected extracts. |
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|
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@author Nicklas |
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@since 3.5 |
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*/ |
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public class PhysicalBioAssayToDerivedBioAssayTransformer |
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extends AbstractSourceItemTransformer |
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{ |
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private CollectExtracts collectedExtracts; |
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|
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/** |
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Create a new physical bioassay to derived bioassay transformer. |
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*/ |
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public PhysicalBioAssayToDerivedBioAssayTransformer() |
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{ |
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super(Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY); |
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} |
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|
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/** |
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Create a new physical bioassay to derived bioassay transformer using |
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the collected extracts to limit the returned items. |
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*/ |
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public PhysicalBioAssayToDerivedBioAssayTransformer(CollectExtracts collectedExtracts) |
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{ |
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this(); |
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this.collectedExtracts = collectedExtracts; |
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} |
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@Override |
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public Set<Integer> transform(TransformContext context, Set<Integer> source) |
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{ |
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DbControl dc = context.getDbControl(); |
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ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery(); |
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query.setIncludes(context.getInclude()); |
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query.join(Hql.innerJoin("physicalBioAssays", "pba")); |
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query.restrict( |
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Restrictions.in( |
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Hql.alias("pba"), |
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Expressions.parameter("bioAssays") |
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) |
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); |
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context.collect(getSourceItemType(), source); |
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Set<Integer> all = context.avoid(getTargetItemType(), safeIdList(dc, query, "bioAssays", source)); |
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if (collectedExtracts != null) |
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{ |
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// Keep only derived bioassays that have a 'null' extract or |
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// an extract that is included among the collected or their parents |
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Set<Integer> collectedAndParents; |
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if (collectedExtracts.getCollectedParents().size() > 0) |
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{ |
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// merge |
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collectedAndParents = new HashSet<Integer>(collectedExtracts.getCollected()); |
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collectedAndParents.addAll(collectedExtracts.getCollectedParents()); |
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} |
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else |
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{ |
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// only use the collected |
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collectedAndParents = collectedExtracts.getCollected(); |
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} |
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query = DerivedBioAssay.getQuery(); |
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query.setIncludes(context.getInclude()); |
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query.join(Hql.leftJoin("extract", "xtr")); |
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query.restrict(Restrictions.or( |
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Restrictions.eq(Hql.alias("xtr"), null), |
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Restrictions.in(Hql.alias("xtr"), Expressions.parameter("extracts")) |
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)); |
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all.retainAll(safeIdList(dc, query, "extracts", collectedAndParents)); |
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} |
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return all; |
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} |
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} |