7005 |
09 Nov 15 |
nicklas |
1 |
/** |
7005 |
09 Nov 15 |
nicklas |
$Id$ |
7005 |
09 Nov 15 |
nicklas |
3 |
|
7005 |
09 Nov 15 |
nicklas |
Copyright (C) 2015 Nicklas Nordborg |
7005 |
09 Nov 15 |
nicklas |
5 |
|
7005 |
09 Nov 15 |
nicklas |
This file is part of BASE - BioArray Software Environment. |
7005 |
09 Nov 15 |
nicklas |
Available at http://base.thep.lu.se/ |
7005 |
09 Nov 15 |
nicklas |
8 |
|
7005 |
09 Nov 15 |
nicklas |
BASE is free software; you can redistribute it and/or |
7005 |
09 Nov 15 |
nicklas |
modify it under the terms of the GNU General Public License |
7005 |
09 Nov 15 |
nicklas |
as published by the Free Software Foundation; either version 3 |
7005 |
09 Nov 15 |
nicklas |
of the License, or (at your option) any later version. |
7005 |
09 Nov 15 |
nicklas |
13 |
|
7005 |
09 Nov 15 |
nicklas |
BASE is distributed in the hope that it will be useful, |
7005 |
09 Nov 15 |
nicklas |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
7005 |
09 Nov 15 |
nicklas |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
7005 |
09 Nov 15 |
nicklas |
GNU General Public License for more details. |
7005 |
09 Nov 15 |
nicklas |
18 |
|
7005 |
09 Nov 15 |
nicklas |
You should have received a copy of the GNU General Public License |
7005 |
09 Nov 15 |
nicklas |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
7005 |
09 Nov 15 |
nicklas |
21 |
*/ |
7005 |
09 Nov 15 |
nicklas |
22 |
package net.sf.basedb.util.overview.validator; |
7005 |
09 Nov 15 |
nicklas |
23 |
|
7005 |
09 Nov 15 |
nicklas |
24 |
import java.util.Date; |
7005 |
09 Nov 15 |
nicklas |
25 |
|
7005 |
09 Nov 15 |
nicklas |
26 |
import net.sf.basedb.core.BasicItem; |
7005 |
09 Nov 15 |
nicklas |
27 |
import net.sf.basedb.core.BioPlateEvent; |
7005 |
09 Nov 15 |
nicklas |
28 |
import net.sf.basedb.core.DateUtil; |
7005 |
09 Nov 15 |
nicklas |
29 |
import net.sf.basedb.core.DbControl; |
7005 |
09 Nov 15 |
nicklas |
30 |
import net.sf.basedb.core.DerivedBioAssay; |
7005 |
09 Nov 15 |
nicklas |
31 |
import net.sf.basedb.core.Item; |
7005 |
09 Nov 15 |
nicklas |
32 |
import net.sf.basedb.core.ItemSubtype; |
7005 |
09 Nov 15 |
nicklas |
33 |
import net.sf.basedb.core.Kit; |
7005 |
09 Nov 15 |
nicklas |
34 |
import net.sf.basedb.core.MeasuredBioMaterial; |
7005 |
09 Nov 15 |
nicklas |
35 |
import net.sf.basedb.core.PermissionDeniedException; |
7005 |
09 Nov 15 |
nicklas |
36 |
import net.sf.basedb.core.PhysicalBioAssay; |
7005 |
09 Nov 15 |
nicklas |
37 |
import net.sf.basedb.core.Subtypable; |
7005 |
09 Nov 15 |
nicklas |
38 |
import net.sf.basedb.core.SystemItems; |
7005 |
09 Nov 15 |
nicklas |
39 |
import net.sf.basedb.util.overview.Fix; |
7005 |
09 Nov 15 |
nicklas |
40 |
import net.sf.basedb.util.overview.OverviewContext; |
7005 |
09 Nov 15 |
nicklas |
41 |
import net.sf.basedb.util.overview.Validator; |
7005 |
09 Nov 15 |
nicklas |
42 |
import net.sf.basedb.util.overview.Node; |
7005 |
09 Nov 15 |
nicklas |
43 |
|
7005 |
09 Nov 15 |
nicklas |
44 |
/** |
7005 |
09 Nov 15 |
nicklas |
Validator implementation for kits. Validation rules: |
7005 |
09 Nov 15 |
nicklas |
<ul> |
7005 |
09 Nov 15 |
nicklas |
<li>Missing item: {@link Validator#MISSING_KIT} |
7005 |
09 Nov 15 |
nicklas |
<li>Access denied: {@link Validator#DENIED_KIT} |
7005 |
09 Nov 15 |
nicklas |
<li>Incorrect hardware type: {@link Validator#INCORRECT_KITTYPE} |
7005 |
09 Nov 15 |
nicklas |
<li>Using kit after expiration date: {@link Validator#KIT_USED_AFTER_EXPIRATIONDATE} |
7005 |
09 Nov 15 |
nicklas |
</ul> |
7005 |
09 Nov 15 |
nicklas |
52 |
|
7005 |
09 Nov 15 |
nicklas |
@author Nicklas |
7005 |
09 Nov 15 |
nicklas |
@since 3.7 |
7005 |
09 Nov 15 |
nicklas |
55 |
*/ |
7005 |
09 Nov 15 |
nicklas |
56 |
public class KitValidator |
7005 |
09 Nov 15 |
nicklas |
57 |
extends NameableNodeValidator<Kit> |
7005 |
09 Nov 15 |
nicklas |
58 |
{ |
7005 |
09 Nov 15 |
nicklas |
59 |
|
7005 |
09 Nov 15 |
nicklas |
60 |
public KitValidator() |
7005 |
09 Nov 15 |
nicklas |
61 |
{ |
7005 |
09 Nov 15 |
nicklas |
62 |
super(null, Validator.DENIED_KIT); |
7005 |
09 Nov 15 |
nicklas |
63 |
} |
7005 |
09 Nov 15 |
nicklas |
64 |
|
7005 |
09 Nov 15 |
nicklas |
65 |
|
7005 |
09 Nov 15 |
nicklas |
66 |
/* |
7005 |
09 Nov 15 |
nicklas |
From BasicValidator class |
7005 |
09 Nov 15 |
nicklas |
68 |
------------------------- |
7005 |
09 Nov 15 |
nicklas |
69 |
*/ |
7005 |
09 Nov 15 |
nicklas |
70 |
/** |
7005 |
09 Nov 15 |
nicklas |
If the parent item has a subtype that is related to a KIT subtype, report |
7005 |
09 Nov 15 |
nicklas |
the missing item as a {@link Validator#MISSING_KIT} failure. Otherwise, |
7005 |
09 Nov 15 |
nicklas |
ignore the missing kit. |
7005 |
09 Nov 15 |
nicklas |
@return Always false |
7005 |
09 Nov 15 |
nicklas |
75 |
*/ |
7005 |
09 Nov 15 |
nicklas |
76 |
@Override |
7005 |
09 Nov 15 |
nicklas |
77 |
public boolean preMissingItem(DbControl dc, OverviewContext context, Node parentNode) |
7005 |
09 Nov 15 |
nicklas |
78 |
{ |
7005 |
09 Nov 15 |
nicklas |
79 |
BasicItem parentItem = parentNode.getItem(dc); |
7005 |
09 Nov 15 |
nicklas |
80 |
ItemSubtype expectedSubtype = getExpectedKitSubtype(dc, parentItem, false); |
7005 |
09 Nov 15 |
nicklas |
81 |
if (expectedSubtype != null) |
7005 |
09 Nov 15 |
nicklas |
82 |
{ |
7005 |
09 Nov 15 |
nicklas |
83 |
context.createFailure(Validator.MISSING_KIT, parentNode, |
7005 |
09 Nov 15 |
nicklas |
84 |
"Missing kit: " + expectedSubtype.getName(), getMissingItemFix(dc, parentNode)); |
7005 |
09 Nov 15 |
nicklas |
85 |
} |
7005 |
09 Nov 15 |
nicklas |
86 |
return false; |
7005 |
09 Nov 15 |
nicklas |
87 |
} |
7005 |
09 Nov 15 |
nicklas |
88 |
|
7005 |
09 Nov 15 |
nicklas |
89 |
/** |
7005 |
09 Nov 15 |
nicklas |
Checks if the hardware is of the correct hardware type |
7005 |
09 Nov 15 |
nicklas |
and, if a project is active, the hardware is included as a |
7005 |
09 Nov 15 |
nicklas |
default hardware for the project. |
7005 |
09 Nov 15 |
nicklas |
93 |
*/ |
7005 |
09 Nov 15 |
nicklas |
94 |
@Override |
7005 |
09 Nov 15 |
nicklas |
95 |
public void postValidate(DbControl dc, OverviewContext context, Node node, Node parentNode) |
7005 |
09 Nov 15 |
nicklas |
96 |
{ |
7005 |
09 Nov 15 |
nicklas |
97 |
super.postValidate(dc, context, node, parentNode); |
7005 |
09 Nov 15 |
nicklas |
98 |
Kit kit = (Kit)node.getItem(dc); |
7005 |
09 Nov 15 |
nicklas |
99 |
|
7005 |
09 Nov 15 |
nicklas |
100 |
BasicItem parentItem = parentNode.getItem(dc); |
7005 |
09 Nov 15 |
nicklas |
101 |
ItemSubtype expectedSubtype = getExpectedKitSubtype(dc, parentItem, true); |
7005 |
09 Nov 15 |
nicklas |
102 |
try |
7005 |
09 Nov 15 |
nicklas |
103 |
{ |
7005 |
09 Nov 15 |
nicklas |
104 |
ItemSubtype subtype = kit.getItemSubtype(); |
7005 |
09 Nov 15 |
nicklas |
105 |
if (expectedSubtype != null && !expectedSubtype.equals(subtype)) |
7005 |
09 Nov 15 |
nicklas |
106 |
{ |
7005 |
09 Nov 15 |
nicklas |
107 |
ItemSubtype mySubtype = ((Subtypable)parentItem).getItemSubtype(); |
7005 |
09 Nov 15 |
nicklas |
108 |
Fix subtypeFix = subtype == null || mySubtype == null ? null : |
7005 |
09 Nov 15 |
nicklas |
109 |
new Fix("Change related kit subtype of '" + mySubtype.getName() + |
7005 |
09 Nov 15 |
nicklas |
110 |
"' to '" + subtype.getName() + "'", mySubtype); |
7005 |
09 Nov 15 |
nicklas |
111 |
|
7005 |
09 Nov 15 |
nicklas |
112 |
context.createFailure(Validator.INCORRECT_KITTYPE, parentNode, |
7005 |
09 Nov 15 |
nicklas |
113 |
"Expected a kit with subtype: " + expectedSubtype.getName(), |
7005 |
09 Nov 15 |
nicklas |
114 |
new Fix("Change kit of '" + parentNode.getTitle() + "'", parentItem), |
7005 |
09 Nov 15 |
nicklas |
115 |
new Fix("Change kit type of '" + kit.getName() + "' to '" + expectedSubtype.getName() + "'", kit), |
7005 |
09 Nov 15 |
nicklas |
116 |
subtypeFix |
7005 |
09 Nov 15 |
nicklas |
117 |
); |
7005 |
09 Nov 15 |
nicklas |
118 |
} |
7005 |
09 Nov 15 |
nicklas |
119 |
} |
7005 |
09 Nov 15 |
nicklas |
120 |
catch (PermissionDeniedException ex) |
7005 |
09 Nov 15 |
nicklas |
121 |
{} |
7005 |
09 Nov 15 |
nicklas |
122 |
|
7005 |
09 Nov 15 |
nicklas |
// Check expiration date |
7005 |
09 Nov 15 |
nicklas |
124 |
Date expirationDate = kit.getExpirationDate(); |
7005 |
09 Nov 15 |
nicklas |
125 |
if (expirationDate != null) |
7005 |
09 Nov 15 |
nicklas |
126 |
{ |
7005 |
09 Nov 15 |
nicklas |
127 |
Date useDate = null; |
7005 |
09 Nov 15 |
nicklas |
128 |
if (parentItem instanceof MeasuredBioMaterial) |
7005 |
09 Nov 15 |
nicklas |
129 |
{ |
7005 |
09 Nov 15 |
nicklas |
130 |
useDate = ((MeasuredBioMaterial)parentItem).getCreationEvent().getEventDate(); |
7005 |
09 Nov 15 |
nicklas |
131 |
} |
7005 |
09 Nov 15 |
nicklas |
132 |
else if (parentItem instanceof PhysicalBioAssay) |
7005 |
09 Nov 15 |
nicklas |
133 |
{ |
7005 |
09 Nov 15 |
nicklas |
134 |
useDate = ((PhysicalBioAssay)parentItem).getCreationEvent().getEventDate(); |
7005 |
09 Nov 15 |
nicklas |
135 |
} |
7005 |
09 Nov 15 |
nicklas |
136 |
else if (parentItem instanceof DerivedBioAssay) |
7005 |
09 Nov 15 |
nicklas |
137 |
{ |
7005 |
09 Nov 15 |
nicklas |
// There is no 'event date' on this item so we can't check this |
7005 |
09 Nov 15 |
nicklas |
139 |
} |
7005 |
09 Nov 15 |
nicklas |
140 |
else if (parentItem instanceof BioPlateEvent) |
7005 |
09 Nov 15 |
nicklas |
141 |
{ |
7005 |
09 Nov 15 |
nicklas |
142 |
useDate = ((BioPlateEvent)parentItem).getEventDate(); |
7005 |
09 Nov 15 |
nicklas |
143 |
} |
7005 |
09 Nov 15 |
nicklas |
144 |
|
7005 |
09 Nov 15 |
nicklas |
145 |
if (useDate != null && useDate.after(expirationDate)) |
7005 |
09 Nov 15 |
nicklas |
146 |
{ |
7005 |
09 Nov 15 |
nicklas |
147 |
context.createFailure(Validator.KIT_USED_AFTER_EXPIRATIONDATE, |
7005 |
09 Nov 15 |
nicklas |
148 |
parentNode, "Kit used after expiration date: " + DateUtil.formatDate(expirationDate), |
7005 |
09 Nov 15 |
nicklas |
149 |
new Fix("Change event date of '" + parentNode.getTitle() + "'", parentItem), |
7005 |
09 Nov 15 |
nicklas |
150 |
new Fix("Change expiration date of kit '" + kit.getName() + "'", kit) |
7005 |
09 Nov 15 |
nicklas |
151 |
); |
7005 |
09 Nov 15 |
nicklas |
152 |
} |
7005 |
09 Nov 15 |
nicklas |
153 |
} |
7005 |
09 Nov 15 |
nicklas |
154 |
} |
7005 |
09 Nov 15 |
nicklas |
155 |
|
7005 |
09 Nov 15 |
nicklas |
156 |
/** |
7005 |
09 Nov 15 |
nicklas |
@return Suggested fix is to add a hardware to the parent item |
7005 |
09 Nov 15 |
nicklas |
158 |
*/ |
7005 |
09 Nov 15 |
nicklas |
159 |
@Override |
7005 |
09 Nov 15 |
nicklas |
160 |
protected Fix getMissingItemFix(DbControl dc, Node parentNode) |
7005 |
09 Nov 15 |
nicklas |
161 |
{ |
7005 |
09 Nov 15 |
nicklas |
162 |
BasicItem parentItem = parentNode.getItem(); |
7005 |
09 Nov 15 |
nicklas |
163 |
return new Fix("Add kit to '" + parentNode.getTitle() + "'", parentItem); |
7005 |
09 Nov 15 |
nicklas |
164 |
} |
7005 |
09 Nov 15 |
nicklas |
165 |
// -------------------------------- |
7005 |
09 Nov 15 |
nicklas |
166 |
|
7005 |
09 Nov 15 |
nicklas |
167 |
|
7005 |
09 Nov 15 |
nicklas |
168 |
/** |
7005 |
09 Nov 15 |
nicklas |
Get the subtype of the associated kit that we expect for the given |
7005 |
09 Nov 15 |
nicklas |
parent item. |
7005 |
09 Nov 15 |
nicklas |
171 |
*/ |
7005 |
09 Nov 15 |
nicklas |
172 |
protected ItemSubtype getExpectedKitSubtype(DbControl dc, BasicItem parentItem, boolean useDefault) |
7005 |
09 Nov 15 |
nicklas |
173 |
{ |
7005 |
09 Nov 15 |
nicklas |
174 |
ItemSubtype expectedSubtype = null; |
7005 |
09 Nov 15 |
nicklas |
175 |
int defaultSubtypeForItemType = SystemItems.getId(Kit.getDefaultSystemId(parentItem.getType())); |
7005 |
09 Nov 15 |
nicklas |
176 |
try |
7005 |
09 Nov 15 |
nicklas |
177 |
{ |
7005 |
09 Nov 15 |
nicklas |
178 |
if (parentItem instanceof Subtypable) |
7005 |
09 Nov 15 |
nicklas |
179 |
{ |
7005 |
09 Nov 15 |
nicklas |
180 |
expectedSubtype = ItemSubtype.getRelatedSubtype(dc, |
7005 |
09 Nov 15 |
nicklas |
181 |
(Subtypable)parentItem, Item.KIT, useDefault ? defaultSubtypeForItemType : 0); |
7005 |
09 Nov 15 |
nicklas |
182 |
} |
7005 |
09 Nov 15 |
nicklas |
183 |
else if (useDefault && defaultSubtypeForItemType != 0) |
7005 |
09 Nov 15 |
nicklas |
184 |
{ |
7005 |
09 Nov 15 |
nicklas |
185 |
expectedSubtype = ItemSubtype.getById(dc, defaultSubtypeForItemType); |
7005 |
09 Nov 15 |
nicklas |
186 |
} |
7005 |
09 Nov 15 |
nicklas |
187 |
} |
7005 |
09 Nov 15 |
nicklas |
188 |
catch (PermissionDeniedException ex) |
7005 |
09 Nov 15 |
nicklas |
189 |
{} |
7005 |
09 Nov 15 |
nicklas |
190 |
return expectedSubtype; |
7005 |
09 Nov 15 |
nicklas |
191 |
} |
7005 |
09 Nov 15 |
nicklas |
192 |
|
7005 |
09 Nov 15 |
nicklas |
193 |
|
7005 |
09 Nov 15 |
nicklas |
194 |
} |