source: branches/3.5-stable/www/lims/arraydesigns/features/index.jsp @ 6949

Last change on this file since 6949 was 6949, checked in by Nicklas Nordborg, 7 years ago

References #1951: Can't create reporter list from Array design features

Port this fix to the BASE 3.5 stable branch so that it can be inlcuded in the next bugfix release.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Date Id
File size: 6.2 KB
Line 
1<%-- $Id: index.jsp 6949 2015-09-10 12:34:16Z nicklas $
2  ------------------------------------------------------------------
3  Copyright (C) 2006 Jari Häkkinen, 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  @version 2.0
24--%>
25<%@ page pageEncoding="UTF-8" session="false"
26  import="net.sf.basedb.core.SessionControl"
27  import="net.sf.basedb.core.DbControl"
28  import="net.sf.basedb.core.Item"
29  import="net.sf.basedb.core.ItemContext"
30  import="net.sf.basedb.core.ItemQuery"
31  import="net.sf.basedb.core.DataQuery"
32  import="net.sf.basedb.core.DataResultIterator"
33  import="net.sf.basedb.core.Permission"
34  import="net.sf.basedb.core.PermissionDeniedException"
35  import="net.sf.basedb.core.ArrayDesign"
36  import="net.sf.basedb.core.data.FeatureData"
37  import="net.sf.basedb.core.data.ReporterData"
38  import="net.sf.basedb.core.query.Hql"
39  import="net.sf.basedb.clients.web.Base"
40  import="net.sf.basedb.clients.web.WebException"
41  import="net.sf.basedb.clients.web.util.HTML"
42  import="net.sf.basedb.util.Values"
43  import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
44  import="net.sf.basedb.core.plugin.GuiContext"
45  import="net.sf.basedb.util.extensions.ExtensionsInvoker"
46  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
47  import="net.sf.basedb.clients.web.extensions.JspContext"
48  import="net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer"
49  import="net.sf.basedb.clients.web.extensions.list.ListColumnUtil"
50  import="java.util.List"
51%>
52<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
53<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
54<%!
55  private static final ItemContext defaultContext = Base.createDefaultContext("position", 
56    "position,externalId,block,row,column,reporter.name,reporter.externalId");
57  private static final Item itemType = Item.FEATURE;
58 
59  private static void registerExportFormatters(ItemContext cc)
60  {
61    cc.setObject("export.formatter.well.row", new WellCoordinateFormatter(true));
62    cc.setObject("export.formatter.well.column", new WellCoordinateFormatter(false));
63  }
64%>
65<%
66final int arrayDesignId = Values.getInt(request.getParameter("arraydesign_id"));
67
68final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
69final String ID = sc.getId();
70final String cmd = request.getParameter("cmd");
71final String root = request.getContextPath()+"/";
72final String listPage = "list_features.jsp?ID="+ID+"&arraydesign_id="+arrayDesignId;
73final String viewPage = "view_feature.jsp?ID="+ID+"&arraydesign_id="+arrayDesignId;
74
75String forward = null;
76String redirect = null;
77String message = null;
78DbControl dc = null;
79
80try
81{
82  if (cmd == null || "List".equals(cmd))
83  {
84    // Display the list page without updatinging the current context
85    Base.getAndSetCurrentContext(sc, itemType, null, defaultContext, true);
86    redirect = listPage;
87  }
88  else if ("UpdateContext".equals(cmd))
89  {
90    // Display the list page after updating the current context from the request parameters
91    Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
92    redirect = listPage;
93  }
94  else if ("LoadContext".equals(cmd))
95  {
96    // Display the list page after loading a saved context
97    int contextId = Values.getInt(request.getParameter("context"));
98    Base.loadContext(sc, contextId, defaultContext);
99    redirect = listPage;
100  }
101  else if ("ViewItem".equals(cmd))
102  {
103    // Display the view page for a single item
104    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
105    forward = viewPage;
106  }
107  else if ("ExportItems".equals(cmd))
108  {
109    // Run an export plugin in a list context
110    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
111    dc = sc.newDbControl();   
112    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
113    final DataQuery<FeatureData> query = arrayDesign.getFeatures();
114    query.join(Hql.leftJoin(null, "reporter", "rpt", null, true));
115    cc.configureQuery(dc, query, true);
116    cc.setQuery(query);
117    registerExportFormatters(cc);
118    JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, GuiContext.list(itemType), null);
119    ExtensionsInvoker listInvoker = ListColumnUtil.useExtensions(jspContext);
120    listInvoker.render(new ListColumnExportRenderer(cc));
121    dc.close();
122    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+features+of+array+design";
123  }
124  else if ("CreateReporterList".equals(cmd))
125  {
126    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
127    dc = sc.newDbControl();   
128    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
129    final DataQuery<ReporterData> query = arrayDesign.getReporters();
130    query.join(Hql.leftJoin("reporter", "rpt"));
131    cc.configureQuery(dc, query, true);
132    dc.close();
133    cc.setQuery(query);
134    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
135      "&cmd=NewItem&addReporters=1&formId=features&fromContext=FEATURE" +
136      "&name=" + HTML.urlEncode(arrayDesign.getName());
137  }
138  else
139  {
140    throw new WebException("popup", "Invalid command", "The command {1} is not recognised as a valid command.", cmd);
141  }
142
143}
144finally
145{
146  if (dc != null) dc.close();
147}
148if (forward != null)
149{
150  sc.setSessionSetting("alert-message", message);
151  pageContext.forward(forward);
152}
153else if (redirect != null)
154{
155  sc.setSessionSetting("alert-message", message);
156  response.sendRedirect(redirect);
157}
158else if (message == null)
159{
160  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&wait=0");
161}
162else
163{
164  response.sendRedirect(root + "common/close_popup.jsp?refresh_opener=1&message="+HTML.urlEncode(message));
165}
166
167%>
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