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/** |
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$Id$ |
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3 |
|
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Copyright (C) 2008 Nicklas Nordborg |
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5 |
|
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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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8 |
|
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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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13 |
|
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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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18 |
|
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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.validator; |
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|
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import java.util.Collections; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.Map; |
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import java.util.Set; |
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|
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import net.sf.basedb.core.BasicItem; |
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import net.sf.basedb.core.BioMaterialEvent; |
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import net.sf.basedb.core.BioMaterialEventSource; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Extract; |
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import net.sf.basedb.core.Include; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemQuery; |
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38 |
import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.core.PermissionDeniedException; |
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import net.sf.basedb.core.PhysicalBioAssay; |
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import net.sf.basedb.core.Sample; |
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import net.sf.basedb.core.SpecialQuery; |
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import net.sf.basedb.core.Tag; |
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import net.sf.basedb.util.EqualsHelper; |
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import net.sf.basedb.util.listable.ExtractToParentExtractTransformer; |
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import net.sf.basedb.util.listable.SourceItemTransformer; |
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import net.sf.basedb.util.listable.TransformContext; |
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import net.sf.basedb.util.overview.Failure; |
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import net.sf.basedb.util.overview.Fix; |
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import net.sf.basedb.util.overview.OverviewContext; |
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import net.sf.basedb.util.overview.Validator; |
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import net.sf.basedb.util.overview.Node; |
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import net.sf.basedb.util.overview.node.ChildNodeDirection; |
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|
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/** |
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Validator implementation for extracts. Validation rules: |
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<ul> |
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<li>Missing item: {@link Validator#MISSING_EXTRACT} |
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<li>Access denied: {@link Validator#DENIED_EXTRACT} |
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<li>Subtype of parent extract: {@link Validator#INCORRECT_EXTRACT_TYPE} |
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<li>Subtype of parent sample: {@link Validator#INCORRECT_SAMPLE_TYPE} |
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<li>Different tag than parent: {@link Validator#DIFFERENT_TAG} |
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<li>Parent is tagged, but child is not: {@link Validator#TAGGED_PARENT} |
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<li>Duplicates of same tag+position on bioassay: {@link Validator#NONUNIQUE_TAG} |
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<li>Incorrect position on bioassay: {@link Validator#INCORRECT_BIOASSAY_POSITION} |
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</ul> |
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67 |
|
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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 ExtractValidator |
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extends NameableNodeValidator<Extract> |
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{ |
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|
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public ExtractValidator() |
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{ |
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super(Validator.MISSING_EXTRACT, Validator.DENIED_EXTRACT); |
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} |
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|
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/* |
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From BasicValidator class |
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------------------------- |
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*/ |
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/** |
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Do not report missing items if the parent node is a derived or (root) raw bioassay. |
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87 |
*/ |
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@Override |
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public boolean preMissingItem(DbControl dc, OverviewContext context, Node parentNode) |
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{ |
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Item parentType = parentNode.getItemType(); |
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if (parentType == Item.DERIVEDBIOASSAY || parentType == Item.RAWBIOASSAY || parentType == Item.ROOTRAWBIOASSAY) return false; |
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return super.preMissingItem(dc, context, parentNode); |
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} |
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95 |
|
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@Override |
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public void postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode) |
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{ |
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super.postValidate(dc, context, node, parentNode); |
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100 |
|
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if (parentNode != null) |
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{ |
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Node parentItemNode = parentNode.getNodeType() == Node.Type.ITEM ? parentNode : parentNode.getParent(); |
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Item parentType = parentItemNode.getItemType(); |
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|
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if (parentType == Item.SAMPLE) |
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{ |
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checkParentSampleSubtype(dc, context, node, parentItemNode); |
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109 |
} |
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else if (parentType == Item.EXTRACT) |
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{ |
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if (node.getChildNodeDirection() == ChildNodeDirection.FORWARD) |
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{ |
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checkParentExtractSubtype(dc, context, node, parentItemNode); |
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checkExtractTag(dc, context, node, parentItemNode); |
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} |
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else |
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{ |
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checkParentExtractSubtype(dc, context, parentItemNode, node); |
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checkExtractTag(dc, context, parentItemNode, node); |
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121 |
} |
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} |
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else if (parentType == Item.PHYSICALBIOASSAY) |
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{ |
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PhysicalBioAssayValidator.checkExtractSubtype(dc, context, parentItemNode, node); |
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checkExtractOnBioAssay(dc, context, node, parentItemNode); |
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} |
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else if (parentType == Item.DERIVEDBIOASSAY) |
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{ |
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DerivedBioAssayValidator.checkExtractSubtype(dc, context, parentItemNode, node); |
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} |
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else if (parentType == Item.BIOPLATE) |
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{ |
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BioPlateValidator.checkBioMaterialInWell(dc, context, parentItemNode, node); |
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} |
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} |
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} |
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|
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|
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/** |
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The suggested fix is to add parent extracts to the physical |
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bioassay or one or more extracts to the pooled extract. |
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*/ |
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144 |
@Override |
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protected Fix getMissingItemFix(DbControl dc, Node parentNode) |
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{ |
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Fix fix = null; |
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Item parentType = parentNode.getItemType(); |
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BasicItem parentItem = parentNode.getItem(); |
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if (parentType == Item.PHYSICALBIOASSAY) |
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{ |
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fix = new Fix("Add extracts to '" + ((PhysicalBioAssay)parentItem).getName() + "'", parentItem); |
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} |
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else if (parentType == Item.EXTRACT) |
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{ |
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fix = new Fix("Add parent extracts to '" + ((Extract)parentItem).getName() + "'", parentItem); |
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} |
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return fix; |
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} |
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|
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161 |
/** |
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If the parent is a physical bioassay, check that extracts on the |
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same position has different tags. |
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164 |
*/ |
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165 |
@SuppressWarnings("unchecked") |
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@Override |
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167 |
public void postValidateFolder(DbControl dc, OverviewContext context, Node folderNode, Node parentNode) |
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{ |
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super.postValidateFolder(dc, context, folderNode, parentNode); |
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if (parentNode.getItemType() != Item.PHYSICALBIOASSAY) return; |
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171 |
|
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172 |
PhysicalBioAssay pba = (PhysicalBioAssay)parentNode.getItem(dc); |
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BioMaterialEvent creationEvent = pba.getCreationEvent(); |
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174 |
|
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// Get all positions that are used by the child nodes |
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176 |
if (folderNode != null) |
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{ |
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// Create a map of tag+position => extract(s) |
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179 |
Map<TagPosition, Set<Extract>> tagPositions = |
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180 |
(Map<TagPosition, Set<Extract>>)context.getCachedObject("TAGPOSITIONS:" + pba.getId()); |
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181 |
if (tagPositions == null) |
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182 |
{ |
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183 |
tagPositions = new HashMap<ExtractValidator.TagPosition, Set<Extract>>(); |
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184 |
context.setCachedObject("TAGPOSITIONS:" + pba.getId(), tagPositions); |
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185 |
|
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186 |
SpecialQuery<BioMaterialEventSource> query = creationEvent.getEventSources(); |
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187 |
for (BioMaterialEventSource src : query.list(dc)) |
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188 |
{ |
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189 |
try |
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190 |
{ |
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191 |
Extract extract = (Extract)src.getBioMaterial(); |
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192 |
Tag tag = extract.getTag(); |
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193 |
int position = src.getPosition(); |
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194 |
TagPosition tp = new TagPosition(tag, position); |
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195 |
Set<Extract> extracts = tagPositions.get(tp); |
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196 |
if (extracts == null) |
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197 |
{ |
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// First extract with this tag+position |
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199 |
extracts = new HashSet<Extract>(); |
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200 |
tagPositions.put(tp, extracts); |
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201 |
} |
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202 |
extracts.add(extract); |
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203 |
} |
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204 |
catch (PermissionDeniedException ex) |
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205 |
{} |
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206 |
} |
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207 |
} |
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208 |
|
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// Get the positions for the extracts in the current folder |
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210 |
Set<Integer> positions = new HashSet<Integer>(); |
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211 |
for (Node extractNode : folderNode.getChildren()) |
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212 |
{ |
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213 |
Extract extract = (Extract)extractNode.getItem(dc); |
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214 |
BioMaterialEventSource src = creationEvent.getEventSource(extract); |
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215 |
positions.add(src.getPosition()); |
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216 |
} |
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217 |
|
5807 |
14 Oct 11 |
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// Check in the map if there are any tag+positions with more than one extract |
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219 |
for (Map.Entry<TagPosition, Set<Extract>> entry : tagPositions.entrySet()) |
5807 |
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220 |
{ |
5807 |
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221 |
Set<Extract> extracts = entry.getValue(); |
5807 |
14 Oct 11 |
nicklas |
222 |
TagPosition tp = entry.getKey(); |
5807 |
14 Oct 11 |
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223 |
if (extracts.size() > 1 && positions.contains(tp.position)) |
5807 |
14 Oct 11 |
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224 |
{ |
5807 |
14 Oct 11 |
nicklas |
// There are duplicates |
5807 |
14 Oct 11 |
nicklas |
226 |
Failure failure = context.createFailure(Validator.NONUNIQUE_TAG, parentNode, |
5807 |
14 Oct 11 |
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227 |
"Multiple extracts on position " + tp.position + " with tag: " + |
5807 |
14 Oct 11 |
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228 |
(tp.tag == null ? "none" : tp.tag.getName())); |
5807 |
14 Oct 11 |
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229 |
if (failure != null) |
5807 |
14 Oct 11 |
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230 |
{ |
5807 |
14 Oct 11 |
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231 |
failure.setDescriptor(tp); |
5807 |
14 Oct 11 |
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232 |
failure.addFix(new Fix("Change extracts on physical bioassay", pba)); |
5807 |
14 Oct 11 |
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233 |
for (Extract e : extracts) |
5807 |
14 Oct 11 |
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234 |
{ |
5807 |
14 Oct 11 |
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235 |
failure.addFix(new Fix("Change tag of '" + e.getName() + "'", e)); |
5807 |
14 Oct 11 |
nicklas |
236 |
} |
5807 |
14 Oct 11 |
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237 |
} |
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238 |
} |
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239 |
} |
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240 |
} |
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241 |
|
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242 |
} |
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243 |
// ---------------------------- |
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08 Jun 11 |
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244 |
|
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08 Jun 11 |
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245 |
|
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08 Jun 11 |
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246 |
/** |
5651 |
08 Jun 11 |
nicklas |
Check the subtype of the sample that is the parent to an extract. Given that |
5651 |
08 Jun 11 |
nicklas |
the extract has a non-null subtype, which has a related SAMPLE subtype, this |
5651 |
08 Jun 11 |
nicklas |
method checks if the parent sample has the same subtype. If there is no related |
5651 |
08 Jun 11 |
nicklas |
subtype for the extract, any subtype for the parent is accepted. |
5651 |
08 Jun 11 |
nicklas |
@since 3.0 |
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08 Jun 11 |
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252 |
*/ |
5651 |
08 Jun 11 |
nicklas |
253 |
public static void checkParentSampleSubtype(DbControl dc, OverviewContext context, Node extractNode, Node sampleNode) |
5651 |
08 Jun 11 |
nicklas |
254 |
{ |
5807 |
14 Oct 11 |
nicklas |
255 |
Extract extract = (Extract)extractNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
256 |
Sample sample = (Sample)sampleNode.getItem(dc); |
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08 Jun 11 |
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257 |
|
5651 |
08 Jun 11 |
nicklas |
258 |
try |
5651 |
08 Jun 11 |
nicklas |
259 |
{ |
5651 |
08 Jun 11 |
nicklas |
260 |
ItemSubtype expectedSubtype = ItemSubtype.getRelatedSubtype(dc, extract, Item.SAMPLE, Item.EXTRACT); |
5651 |
08 Jun 11 |
nicklas |
261 |
ItemSubtype subtype = sample.getItemSubtype(); |
5651 |
08 Jun 11 |
nicklas |
262 |
|
5651 |
08 Jun 11 |
nicklas |
263 |
if (expectedSubtype != null && !expectedSubtype.equals(subtype)) |
5651 |
08 Jun 11 |
nicklas |
264 |
{ |
5807 |
14 Oct 11 |
nicklas |
265 |
ItemSubtype mySubtype = extract.getItemSubtype(); |
5807 |
14 Oct 11 |
nicklas |
266 |
Fix subtypeFix = subtype == null ? null : |
5807 |
14 Oct 11 |
nicklas |
267 |
new Fix("Change related sample subtype of '" + mySubtype.getName() + |
5807 |
14 Oct 11 |
nicklas |
268 |
"' to '" + subtype.getName() + "'", mySubtype); |
5651 |
08 Jun 11 |
nicklas |
269 |
if (expectedSubtype.getMainItemType() == Item.SAMPLE) |
5651 |
08 Jun 11 |
nicklas |
270 |
{ |
5651 |
08 Jun 11 |
nicklas |
271 |
context.createFailure(Validator.INCORRECT_SAMPLE_TYPE, extractNode, |
5807 |
14 Oct 11 |
nicklas |
272 |
"Expected a sample with subtype: " + expectedSubtype.getName(), |
5807 |
14 Oct 11 |
nicklas |
273 |
new Fix("Change subtype of '" + sample.getName() + "' to '" + expectedSubtype.getName() + "'", sample), |
5807 |
14 Oct 11 |
nicklas |
274 |
new Fix("Change subtype or parent sample of '" + extractNode.getTitle() + "'", extract), |
5807 |
14 Oct 11 |
nicklas |
275 |
subtypeFix |
5651 |
08 Jun 11 |
nicklas |
276 |
); |
5651 |
08 Jun 11 |
nicklas |
277 |
} |
5651 |
08 Jun 11 |
nicklas |
278 |
else |
5651 |
08 Jun 11 |
nicklas |
279 |
{ |
5651 |
08 Jun 11 |
nicklas |
280 |
context.createFailure(Validator.INCORRECT_SAMPLE_TYPE, extractNode, |
5807 |
14 Oct 11 |
nicklas |
281 |
"Expected an extract with subtype: " + expectedSubtype.getName(), |
5807 |
14 Oct 11 |
nicklas |
282 |
new Fix("Change subtype or parent of '" + extractNode.getTitle() + "'", extract), |
5807 |
14 Oct 11 |
nicklas |
283 |
subtypeFix |
5651 |
08 Jun 11 |
nicklas |
284 |
); |
5651 |
08 Jun 11 |
nicklas |
285 |
} |
5651 |
08 Jun 11 |
nicklas |
286 |
} |
5651 |
08 Jun 11 |
nicklas |
287 |
} |
5651 |
08 Jun 11 |
nicklas |
288 |
catch (PermissionDeniedException ex) |
5651 |
08 Jun 11 |
nicklas |
289 |
{} |
5651 |
08 Jun 11 |
nicklas |
290 |
} |
5651 |
08 Jun 11 |
nicklas |
291 |
|
5651 |
08 Jun 11 |
nicklas |
292 |
/** |
5651 |
08 Jun 11 |
nicklas |
Check the subtype of the extract that is the parent to another extract. Given that |
5651 |
08 Jun 11 |
nicklas |
the child extract has a non-null subtype, which has a related EXTRACT subtype, this |
5651 |
08 Jun 11 |
nicklas |
method checks if the parent extract has the same subtype. If there is no related |
5651 |
08 Jun 11 |
nicklas |
subtype for the child extract, any subtype for the parent is accepted. |
5651 |
08 Jun 11 |
nicklas |
@since 3.0 |
5651 |
08 Jun 11 |
nicklas |
298 |
*/ |
5651 |
08 Jun 11 |
nicklas |
299 |
public static void checkParentExtractSubtype(DbControl dc, OverviewContext context, Node childNode, Node parentNode) |
5651 |
08 Jun 11 |
nicklas |
300 |
{ |
5807 |
14 Oct 11 |
nicklas |
301 |
Extract child = (Extract)childNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
302 |
Extract parent = (Extract)parentNode.getItem(dc); |
5651 |
08 Jun 11 |
nicklas |
303 |
|
5651 |
08 Jun 11 |
nicklas |
304 |
try |
5651 |
08 Jun 11 |
nicklas |
305 |
{ |
5807 |
14 Oct 11 |
nicklas |
306 |
ItemSubtype expectedSubtype = ItemSubtype.getRelatedSubtype(dc, child, Item.EXTRACT, Item.SAMPLE); |
5651 |
08 Jun 11 |
nicklas |
307 |
ItemSubtype subtype = parent.getItemSubtype(); |
5651 |
08 Jun 11 |
nicklas |
308 |
|
5651 |
08 Jun 11 |
nicklas |
309 |
if (expectedSubtype != null && !expectedSubtype.equals(subtype)) |
5651 |
08 Jun 11 |
nicklas |
310 |
{ |
5807 |
14 Oct 11 |
nicklas |
311 |
ItemSubtype mySubtype = child.getItemSubtype(); |
5807 |
14 Oct 11 |
nicklas |
312 |
Fix subtypeFix = subtype == null || subtype.equals(mySubtype) ? null : |
5807 |
14 Oct 11 |
nicklas |
313 |
new Fix("Change related extract subtype of '" + mySubtype.getName() + |
5807 |
14 Oct 11 |
nicklas |
314 |
"' to '" + subtype.getName() + "'", mySubtype); |
5807 |
14 Oct 11 |
nicklas |
315 |
if (expectedSubtype.getMainItemType() == Item.EXTRACT) |
5807 |
14 Oct 11 |
nicklas |
316 |
{ |
5807 |
14 Oct 11 |
nicklas |
317 |
context.createFailure(Validator.INCORRECT_EXTRACT_TYPE, childNode, |
5807 |
14 Oct 11 |
nicklas |
318 |
"Expected an extract with subtype: " + expectedSubtype.getName(), |
5807 |
14 Oct 11 |
nicklas |
319 |
new Fix("Change subtype of '" + parent.getName() + "' to '" + expectedSubtype.getName() + "'", parent), |
5807 |
14 Oct 11 |
nicklas |
320 |
new Fix("Change subtype or parent extract of '" + childNode.getTitle() + "'", child), |
5807 |
14 Oct 11 |
nicklas |
321 |
subtypeFix |
5807 |
14 Oct 11 |
nicklas |
322 |
); |
5807 |
14 Oct 11 |
nicklas |
323 |
} |
5807 |
14 Oct 11 |
nicklas |
324 |
else |
5807 |
14 Oct 11 |
nicklas |
325 |
{ |
5807 |
14 Oct 11 |
nicklas |
326 |
context.createFailure(Validator.INCORRECT_EXTRACT_TYPE, childNode, |
5807 |
14 Oct 11 |
nicklas |
327 |
"Expected a sample with subtype: " + expectedSubtype.getName(), |
5807 |
14 Oct 11 |
nicklas |
328 |
new Fix("Change subtype or parent of '" + childNode.getTitle() + "'", child), |
5807 |
14 Oct 11 |
nicklas |
329 |
subtypeFix |
5807 |
14 Oct 11 |
nicklas |
330 |
); |
5807 |
14 Oct 11 |
nicklas |
331 |
|
5807 |
14 Oct 11 |
nicklas |
332 |
} |
5651 |
08 Jun 11 |
nicklas |
333 |
} |
5651 |
08 Jun 11 |
nicklas |
334 |
} |
5651 |
08 Jun 11 |
nicklas |
335 |
catch (PermissionDeniedException ex) |
5651 |
08 Jun 11 |
nicklas |
336 |
{} |
5651 |
08 Jun 11 |
nicklas |
337 |
} |
5651 |
08 Jun 11 |
nicklas |
338 |
|
5807 |
14 Oct 11 |
nicklas |
339 |
/** |
5807 |
14 Oct 11 |
nicklas |
Check the tag of the child extract in relation to a parent extract. If the parent |
5807 |
14 Oct 11 |
nicklas |
extract has a tag, the child must have the same tag. If the parent is not |
5807 |
14 Oct 11 |
nicklas |
tagged, then the child may have any tag or no tag. |
5807 |
14 Oct 11 |
nicklas |
@since 3.0 |
5807 |
14 Oct 11 |
nicklas |
344 |
*/ |
5807 |
14 Oct 11 |
nicklas |
345 |
public static void checkExtractTag(DbControl dc, OverviewContext context, Node childNode, Node parentNode) |
5807 |
14 Oct 11 |
nicklas |
346 |
{ |
5807 |
14 Oct 11 |
nicklas |
347 |
Extract child = (Extract)childNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
348 |
Extract parent = (Extract)parentNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
349 |
|
5807 |
14 Oct 11 |
nicklas |
350 |
try |
5807 |
14 Oct 11 |
nicklas |
351 |
{ |
5807 |
14 Oct 11 |
nicklas |
352 |
Tag parentTag = parent.getTag(); |
5807 |
14 Oct 11 |
nicklas |
353 |
if (parentTag != null) |
5807 |
14 Oct 11 |
nicklas |
354 |
{ |
5807 |
14 Oct 11 |
nicklas |
355 |
Tag childTag = child.getTag(); |
5807 |
14 Oct 11 |
nicklas |
356 |
if (!parentTag.equals(childTag)) |
5807 |
14 Oct 11 |
nicklas |
357 |
{ |
5807 |
14 Oct 11 |
nicklas |
358 |
if (childTag != null) |
5807 |
14 Oct 11 |
nicklas |
359 |
{ |
5807 |
14 Oct 11 |
nicklas |
360 |
context.createFailure(Validator.DIFFERENT_TAG, childNode, |
5807 |
14 Oct 11 |
nicklas |
361 |
"Extract '" + child.getName() + "' has tag mismatch: " + childTag.getName(), |
5807 |
14 Oct 11 |
nicklas |
362 |
new Fix("Change tag of '" + child.getName() + "' to '" + parentTag.getName() + "'", child), |
5807 |
14 Oct 11 |
nicklas |
363 |
new Fix("Change tag of '" + parent.getName() + "' to '" + childTag.getName() + "'", parent) |
5807 |
14 Oct 11 |
nicklas |
364 |
); |
5807 |
14 Oct 11 |
nicklas |
365 |
} |
5807 |
14 Oct 11 |
nicklas |
366 |
else |
5807 |
14 Oct 11 |
nicklas |
367 |
{ |
5807 |
14 Oct 11 |
nicklas |
368 |
context.createFailure(Validator.TAGGED_PARENT, childNode, |
5807 |
14 Oct 11 |
nicklas |
369 |
"Extract '" + child.getName() + "' has no tag but parent has", |
5807 |
14 Oct 11 |
nicklas |
370 |
new Fix("Change tag of '" + child.getName() + "' to '" + parentTag.getName() + "'", child), |
5807 |
14 Oct 11 |
nicklas |
371 |
new Fix("Remove tag from '" + parent.getName() + "'", parent) |
5807 |
14 Oct 11 |
nicklas |
372 |
); |
5807 |
14 Oct 11 |
nicklas |
373 |
} |
5807 |
14 Oct 11 |
nicklas |
374 |
|
5807 |
14 Oct 11 |
nicklas |
375 |
} |
5807 |
14 Oct 11 |
nicklas |
376 |
} |
5807 |
14 Oct 11 |
nicklas |
377 |
} |
5807 |
14 Oct 11 |
nicklas |
378 |
catch (PermissionDeniedException ex) |
5807 |
14 Oct 11 |
nicklas |
379 |
{} |
5807 |
14 Oct 11 |
nicklas |
380 |
} |
5807 |
14 Oct 11 |
nicklas |
381 |
|
6098 |
03 Sep 12 |
nicklas |
382 |
/** |
6098 |
03 Sep 12 |
nicklas |
Check if two given extracts have a parent-child relationship. |
6098 |
03 Sep 12 |
nicklas |
@since 3.2 |
6098 |
03 Sep 12 |
nicklas |
385 |
*/ |
6098 |
03 Sep 12 |
nicklas |
386 |
@SuppressWarnings("unchecked") |
6098 |
03 Sep 12 |
nicklas |
387 |
public static boolean isRelated(DbControl dc, OverviewContext context, Extract parent, Extract child) |
6098 |
03 Sep 12 |
nicklas |
388 |
{ |
6100 |
04 Sep 12 |
nicklas |
// Short-cut if both extracts are the same |
6100 |
04 Sep 12 |
nicklas |
390 |
if (child.equals(parent)) return true; |
6100 |
04 Sep 12 |
nicklas |
391 |
|
6098 |
03 Sep 12 |
nicklas |
392 |
String cacheKey = "extract." + child.getId() + ".parents"; |
6799 |
25 Mar 15 |
nicklas |
393 |
Set<Integer> allParents = (Set<Integer>)context.getCachedObject(cacheKey); |
6098 |
03 Sep 12 |
nicklas |
394 |
|
6098 |
03 Sep 12 |
nicklas |
395 |
if (allParents == null) |
6098 |
03 Sep 12 |
nicklas |
396 |
{ |
6098 |
03 Sep 12 |
nicklas |
397 |
if (child.getParentType() == Item.EXTRACT) |
6098 |
03 Sep 12 |
nicklas |
398 |
{ |
7605 |
26 Feb 19 |
nicklas |
399 |
ItemQuery<Extract> query = child.getCreationEvent().getSources(); |
6098 |
03 Sep 12 |
nicklas |
400 |
query.include(Include.ALL); |
6799 |
25 Mar 15 |
nicklas |
401 |
SourceItemTransformer transformer = new ExtractToParentExtractTransformer(true); |
6799 |
25 Mar 15 |
nicklas |
402 |
allParents = transformer.transform(new TransformContext(dc), new HashSet<Integer>(query.idList(dc))); |
6098 |
03 Sep 12 |
nicklas |
403 |
} |
6098 |
03 Sep 12 |
nicklas |
404 |
else |
6098 |
03 Sep 12 |
nicklas |
405 |
{ |
6098 |
03 Sep 12 |
nicklas |
406 |
allParents = Collections.emptySet(); |
6098 |
03 Sep 12 |
nicklas |
407 |
} |
6098 |
03 Sep 12 |
nicklas |
408 |
context.setCachedObject(cacheKey, allParents); |
6098 |
03 Sep 12 |
nicklas |
409 |
} |
6799 |
25 Mar 15 |
nicklas |
410 |
return allParents.contains(parent.getId()); |
6098 |
03 Sep 12 |
nicklas |
411 |
} |
5807 |
14 Oct 11 |
nicklas |
412 |
|
5807 |
14 Oct 11 |
nicklas |
413 |
private void checkExtractOnBioAssay(DbControl dc, OverviewContext context, Node extractNode, Node bioAssayNode) |
5807 |
14 Oct 11 |
nicklas |
414 |
{ |
5807 |
14 Oct 11 |
nicklas |
// Check that the extract's position is within the expected range |
5807 |
14 Oct 11 |
nicklas |
416 |
PhysicalBioAssay bioAssay = (PhysicalBioAssay)bioAssayNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
417 |
int bioAssaySize = bioAssay.getSize(); |
5807 |
14 Oct 11 |
nicklas |
418 |
Extract extract = (Extract)extractNode.getItem(dc); |
5807 |
14 Oct 11 |
nicklas |
419 |
BioMaterialEventSource src = bioAssay.getCreationEvent().getEventSource(extract); |
5807 |
14 Oct 11 |
nicklas |
420 |
int position = src.getPosition(); |
5807 |
14 Oct 11 |
nicklas |
421 |
if (position > bioAssaySize || position < 1) |
5807 |
14 Oct 11 |
nicklas |
422 |
{ |
5813 |
18 Oct 11 |
nicklas |
423 |
context.createFailure(Validator.INCORRECT_BIOASSAY_POSITION, bioAssayNode, |
5813 |
18 Oct 11 |
nicklas |
424 |
"Incorrect position for '" + extract.getName() + "': " + |
5813 |
18 Oct 11 |
nicklas |
425 |
position + " (expected 1.." + bioAssaySize + ")", |
5813 |
18 Oct 11 |
nicklas |
426 |
new Fix("Change position for extract: " + extract.getName(), bioAssay), |
5807 |
14 Oct 11 |
nicklas |
427 |
position <= 0 ? null : new Fix("Increase size of physical bioassay", bioAssay)); |
5807 |
14 Oct 11 |
nicklas |
428 |
} |
5807 |
14 Oct 11 |
nicklas |
429 |
} |
5651 |
08 Jun 11 |
nicklas |
430 |
|
5807 |
14 Oct 11 |
nicklas |
431 |
|
5807 |
14 Oct 11 |
nicklas |
432 |
static class TagPosition |
5807 |
14 Oct 11 |
nicklas |
433 |
{ |
5807 |
14 Oct 11 |
nicklas |
434 |
final Tag tag; |
5807 |
14 Oct 11 |
nicklas |
435 |
final int position; |
5807 |
14 Oct 11 |
nicklas |
436 |
|
5807 |
14 Oct 11 |
nicklas |
437 |
TagPosition(Tag tag, int position) |
5807 |
14 Oct 11 |
nicklas |
438 |
{ |
5807 |
14 Oct 11 |
nicklas |
439 |
this.tag = tag; |
5807 |
14 Oct 11 |
nicklas |
440 |
this.position = position; |
5807 |
14 Oct 11 |
nicklas |
441 |
} |
5807 |
14 Oct 11 |
nicklas |
442 |
|
5807 |
14 Oct 11 |
nicklas |
443 |
@Override |
5807 |
14 Oct 11 |
nicklas |
444 |
public int hashCode() |
5807 |
14 Oct 11 |
nicklas |
445 |
{ |
5807 |
14 Oct 11 |
nicklas |
446 |
return EqualsHelper.hashCode(tag) + position; |
5807 |
14 Oct 11 |
nicklas |
447 |
} |
5807 |
14 Oct 11 |
nicklas |
448 |
|
5807 |
14 Oct 11 |
nicklas |
449 |
@Override |
5807 |
14 Oct 11 |
nicklas |
450 |
public boolean equals(Object o) |
5807 |
14 Oct 11 |
nicklas |
451 |
{ |
5807 |
14 Oct 11 |
nicklas |
452 |
TagPosition other = (TagPosition)o; |
5807 |
14 Oct 11 |
nicklas |
453 |
return EqualsHelper.equals(this.tag, other.tag) && this.position == other.position; |
5807 |
14 Oct 11 |
nicklas |
454 |
} |
5807 |
14 Oct 11 |
nicklas |
455 |
|
5807 |
14 Oct 11 |
nicklas |
456 |
} |
5807 |
14 Oct 11 |
nicklas |
457 |
|
4740 |
05 Feb 09 |
nicklas |
458 |
} |