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/** |
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$Id$ |
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Copyright (C) 2008 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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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.overview.loader; |
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|
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import net.sf.basedb.core.ArrayBatch; |
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import net.sf.basedb.core.ArrayDesign; |
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import net.sf.basedb.core.BasicItem; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.PermissionDeniedException; |
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import net.sf.basedb.core.RawBioAssay; |
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import net.sf.basedb.core.RootRawBioAssay; |
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import net.sf.basedb.util.overview.OverviewContext; |
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import net.sf.basedb.util.overview.node.ChildNodeDirection; |
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import net.sf.basedb.util.overview.node.NameableNameGenerator; |
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import net.sf.basedb.util.overview.Node; |
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import net.sf.basedb.util.overview.node.NodeFactory; |
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/** |
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Node loader implementation for array designs. Array designs are |
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an endpoint node with the forward-loading direction going to |
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{@link ArrayDesign}:s -> {@link ArrayBatch}:s. An array design can |
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also be loaded as a property node from a raw bioassay. |
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|
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@author Nicklas |
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@version 2.10 |
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@base.modified $Date$ |
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*/ |
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public class ArrayDesignLoader |
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extends BasicItemNodeLoader<ArrayDesign> |
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{ |
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|
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public ArrayDesignLoader() |
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{ |
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super(Item.ARRAYDESIGN, ALLOW_ROOT_NODE, |
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new NameableNameGenerator<ArrayDesign>("arraydesign", "Array design")); |
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} |
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|
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/* |
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From the NodeLoader interface |
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------------------------------ |
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*/ |
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/** |
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Create a reverse-loading array design node from an array batch node. |
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@return An array design node, or null if the batch doesn't have a design |
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*/ |
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@Override |
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public Node createReverseNode(DbControl dc, OverviewContext context, Node batchNode) |
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{ |
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NodeFactory<ArrayDesign> nf = getNodeFactory(dc, context); |
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ArrayDesign design = null; |
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boolean denied = false; |
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try |
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{ |
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design = ((ArrayBatch)batchNode.getItem(dc)).getArrayDesign(); |
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} |
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catch (PermissionDeniedException ex) |
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{ |
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denied = true; |
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} |
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Node designNode = createItemNode(nf, design, design, denied, |
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batchNode, ChildNodeDirection.REVERSE); |
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return designNode; |
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} |
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/** |
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Create an array design property node from a raw bioassay or |
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root raw bioassay node. |
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@return An array design node, or null if the raw bioassay doesn't have a design |
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*/ |
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@Override |
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public Node createPropertyNode(DbControl dc, OverviewContext context, Node parentNode) |
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{ |
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NodeFactory<ArrayDesign> nf = getNodeFactory(dc, context); |
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ArrayDesign design = null; |
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boolean denied = false; |
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try |
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{ |
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BasicItem parentItem = parentNode.getItem(dc); |
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if (parentItem instanceof RootRawBioAssay) |
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{ |
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// The parent may be a root raw bioasay if the overview starts at the |
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// experiment level |
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parentItem = ((RootRawBioAssay)parentItem).getRawBioAssay(); |
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} |
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if (parentItem instanceof RawBioAssay) |
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{ |
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RawBioAssay rba = (RawBioAssay)parentItem; |
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design = rba.getArrayDesign(); |
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} |
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} |
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catch (PermissionDeniedException ex) |
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{ |
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denied = true; |
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} |
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Node designNode = createItemNode(nf, design, design, denied, |
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parentNode, ChildNodeDirection.PROPERTY); |
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return designNode; |
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} |
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// -------------------------------- |
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/* |
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From the AbstractNodeLoader class |
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---------------------------------- |
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*/ |
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/** |
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Loads property nodes of an array design. |
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<ul> |
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<li>Annotations: {@link AnnotationLoader#createPropertyNode(DbControl, OverviewContext, Node)} |
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<li>Data files: {@link DataFileLoader#createPropertyNode(DbControl, OverviewContext, Node)} |
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<li>Platform: {@link PlatformLoader#createPropertyNode(DbControl, OverviewContext, Node)} |
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</ul> |
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*/ |
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@Override |
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protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node designNode) |
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{ |
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getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, designNode); |
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getNodeLoader(context, Item.PLATFORM).createPropertyNode(dc, context, designNode); |
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getNodeLoader(context, Item.FILESETMEMBER).createPropertyNode(dc, context, designNode); |
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getNodeLoader(context, Item.ANYTOANY).createPropertyNode(dc, context, designNode); |
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} |
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|
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/** |
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Loads the array batch nodes that has been created with the given design node. |
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@see ArrayBatchLoader#createForwardNode(DbControl, OverviewContext, Node) |
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*/ |
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@Override |
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protected void loadForwardChildNodes(DbControl dc, OverviewContext context, Node designNode) |
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{ |
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getNodeLoader(context, Item.ARRAYBATCH).createForwardNode(dc, context, designNode); |
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} |
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// --------------------------------------- |
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|
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} |