source: trunk/www/biomaterials/wizards/index.jsp @ 5541

Last change on this file since 5541 was 5541, checked in by Nicklas Nordborg, 12 years ago

References #1564: Move biomaterial on plates

  • Added support for using a predefined plate mapping when moving biomaterial.
  • Display mapped well coordinates on the destination plate.
  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 7.8 KB
Line 
1<%-- $Id: index.jsp 5541 2011-01-17 10:00:42Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) 2010 Nicklas Nordborg
4
5  This file is part of BASE - BioArray Software Environment.
6  Available at http://base.thep.lu.se/
7
8  BASE is free software; you can redistribute it and/or
9  modify it under the terms of the GNU General Public License
10  as published by the Free Software Foundation; either version 3
11  of the License, or (at your option) any later version.
12
13  BASE is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
16  GNU General Public License for more details.
17
18  You should have received a copy of the GNU General Public License
19  along with BASE. If not, see <http://www.gnu.org/licenses/>.
20  ------------------------------------------------------------------
21
22  @author Nicklas
23--%>
24<%@ page pageEncoding="UTF-8" session="false"
25  import="net.sf.basedb.core.SessionControl"
26  import="net.sf.basedb.core.BioMaterial"
27  import="net.sf.basedb.core.BioMaterialEvent"
28  import="net.sf.basedb.core.BioPlate"
29  import="net.sf.basedb.core.BioPlateEvent"
30  import="net.sf.basedb.core.BioPlateEventType"
31  import="net.sf.basedb.core.BioPlateEventParticipant"
32  import="net.sf.basedb.core.BioWell"
33  import="net.sf.basedb.core.DbControl"
34  import="net.sf.basedb.core.Item"
35  import="net.sf.basedb.core.ItemContext"
36  import="net.sf.basedb.core.MeasuredBioMaterial"
37  import="net.sf.basedb.core.Hardware"
38  import="net.sf.basedb.core.Protocol"
39  import="net.sf.basedb.core.PlateGeometry"
40  import="net.sf.basedb.clients.web.Base"
41  import="net.sf.basedb.clients.web.WebException"
42  import="net.sf.basedb.util.Values"
43  import="net.sf.basedb.util.formatter.Formatter"
44  import="net.sf.basedb.clients.web.formatter.FormatterFactory"
45  import="net.sf.basedb.clients.web.formatter.FormatterSettings"
46  import="net.sf.basedb.clients.web.util.HTML"
47  import="java.util.Set"
48  import="java.util.Date"
49%>
50<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
51<%
52final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
53final String ID = sc.getId();
54final String cmd = request.getParameter("cmd");
55final String root = request.getContextPath()+"/";
56final String mode = request.getParameter("mode");
57final String callback = request.getParameter("callback");
58String forward = null;
59String redirect = null;
60String message = null;
61DbControl dc = null;
62
63try
64{
65  if ("PlaceOnPlate".equals(cmd))
66  {
67    dc = sc.newDbControl();
68    Item bioMaterialType = Item.valueOf(request.getParameter("itemType"));
69    String subContext = Values.getString(request.getParameter("subcontext"), "");
70    ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.PLACE_ON_PLATE);
71    final int maxRecent = Base.getMaxRecent(sc);
72
73    sc.setUserClientSetting("place-on-plate.auto-select-unmapped-item", 
74        Values.getBoolean(request.getParameter("autoSelectUnmappedItem")) ? "1" : "0");
75    BioPlate plate = BioPlate.getById(dc, Values.getInt(request.getParameter("plate_id")));
76    int rows = Values.getInt(request.getParameter("rows"));
77    int columns = Values.getInt(request.getParameter("columns"));
78   
79    BioPlateEventType placeOnPlate = BioPlateEventType.getById(dc, BioPlateEventType.PLACE_ON_PLATE);
80    BioPlateEvent event = BioPlateEvent.getNew(dc, placeOnPlate);
81    BioPlateEventParticipant destination = event.addParticipant(plate, "destination", 1);
82   
83    event.setName(Values.getStringOrNull(request.getParameter("name")));
84    event.setDescription(Values.getStringOrNull(request.getParameter("description")));
85    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
86    event.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
87    int protocolId = Values.getInt(request.getParameter("protocol_id"));
88    if (protocolId > 0) 
89    {
90      Protocol pt = Protocol.getById(dc, protocolId);
91      event.setProtocol(pt);
92      cc.setRecent(pt, maxRecent);
93    }
94    int hardwareId = Values.getInt(request.getParameter("hardware_id"));
95    if (hardwareId > 0)
96    {
97      Hardware hw = Hardware.getById(dc, hardwareId);
98      event.setHardware(hw);
99      cc.setRecent(hw, maxRecent);
100    }
101    dc.saveItem(event);
102   
103    int numPlaced = 0;
104    for (int row = 0; row < rows; ++row)
105    {
106      for (int column = 0; column < columns; ++column)
107      {
108        int bioMaterialId = Values.getInt(request.getParameter("well." + row + "." + column));
109        if (bioMaterialId > 0)
110        {
111          MeasuredBioMaterial bioMaterial = (MeasuredBioMaterial)bioMaterialType.getById(dc, bioMaterialId);
112          BioWell well = plate.getBioWell(row, column);
113          bioMaterial.setBioWell(well);
114          BioMaterialEvent bmEvent = bioMaterial.newEvent(destination);
115          bmEvent.setComment("Well: " + well.getCoordinate());
116          dc.saveItem(bmEvent);
117          numPlaced++;
118        }
119      }
120    }
121   
122    dc.commit();
123    message = "Placed " + numPlaced + " items on plate " + plate.getName();
124  }
125  else if ("MoveBioMaterial".equals(cmd))
126  {
127    dc = sc.newDbControl();
128    ItemContext cc = sc.getCurrentContext(Item.BIOPLATEEVENT, BioPlateEventType.MOVE);
129    final int maxRecent = Base.getMaxRecent(sc);
130    sc.setUserClientSetting("move-biomaterial.show-source-coordinates", 
131        Values.getBoolean(request.getParameter("showSourceCoordinates")) ? "1" : "0");
132
133    BioPlate sourcePlate = BioPlate.getById(dc, Values.getInt(request.getParameter("sourceplate_id")));
134    BioPlate destPlate = BioPlate.getById(dc, Values.getInt(request.getParameter("destplate_id")));
135    int rows = Values.getInt(request.getParameter("rows"));
136    int columns = Values.getInt(request.getParameter("columns"));
137   
138    BioPlateEventType moveBioMaterial = BioPlateEventType.getById(dc, BioPlateEventType.MOVE);
139    BioPlateEvent event = BioPlateEvent.getNew(dc, moveBioMaterial);
140    BioPlateEventParticipant destination = event.addParticipant(destPlate, "destination", 1);
141    BioPlateEventParticipant source = event.addParticipant(sourcePlate, "source", 1);
142   
143    event.setName(Values.getStringOrNull(request.getParameter("name")));
144    event.setDescription(Values.getStringOrNull(request.getParameter("description")));
145    Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
146    event.setEventDate(dateFormatter.parseString(Values.getStringOrNull(request.getParameter("event_date"))));
147    int protocolId = Values.getInt(request.getParameter("protocol_id"));
148    if (protocolId > 0) 
149    {
150      Protocol pt = Protocol.getById(dc, protocolId);
151      event.setProtocol(pt);
152      cc.setRecent(pt, maxRecent);
153    }
154    int hardwareId = Values.getInt(request.getParameter("hardware_id"));
155    if (hardwareId > 0)
156    {
157      Hardware hw = Hardware.getById(dc, hardwareId);
158      event.setHardware(hw);
159      cc.setRecent(hw, maxRecent);
160    }
161    dc.saveItem(event);
162   
163    int numMoved = 0;
164    for (int row = 0; row < rows; ++row)
165    {
166      for (int column = 0; column < columns; ++column)
167      {
168        int bioMaterialId = Values.getInt(request.getParameter("well." + row + "." + column));
169        if (bioMaterialId > 0)
170        {
171          MeasuredBioMaterial bioMaterial = (MeasuredBioMaterial)BioMaterial.getById(dc, bioMaterialId);
172          BioWell well = destPlate.getBioWell(row, column);
173          bioMaterial.setBioWell(well);
174          BioMaterialEvent bmEvent = bioMaterial.newEvent(destination);
175          bmEvent.setComment("Well: " + well.getCoordinate());
176          dc.saveItem(bmEvent);
177          numMoved++;
178        }
179      }
180    }
181   
182    dc.commit();
183    message = "Moved " + numMoved + " items to plate " + destPlate.getName();
184  }
185  else
186  {
187    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
188  }
189}
190finally
191{
192  if (dc != null) dc.close();
193}
194
195if (forward != null)
196{
197  pageContext.forward(forward);
198}
199else if (redirect != null)
200{
201  response.sendRedirect(redirect);
202}
203else if (message == null)
204{
205  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
206}
207else
208{
209  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
210}
211%>
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