1 | <%-- $Id: view_rawbioassay.jsp 5939 2012-01-30 14:42:18Z nicklas $ |
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2 | ------------------------------------------------------------------ |
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3 | Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg, Martin Svensson |
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4 | Copyright (C) 2007 Martin Svensson |
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5 | |
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6 | This file is part of BASE - BioArray Software Environment. |
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7 | Available at http://base.thep.lu.se/ |
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8 | |
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9 | BASE is free software; you can redistribute it and/or |
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10 | modify it under the terms of the GNU General Public License |
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11 | as published by the Free Software Foundation; either version 3 |
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12 | of the License, or (at your option) any later version. |
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13 | |
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14 | BASE is distributed in the hope that it will be useful, |
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15 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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17 | GNU General Public License for more details. |
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18 | |
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19 | You should have received a copy of the GNU General Public License |
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20 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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21 | ------------------------------------------------------------------ |
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22 | |
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23 | @author Nicklas |
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24 | @version 2.0 |
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25 | --%> |
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26 | <%@ page pageEncoding="UTF-8" session="false" |
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27 | buffer="500kb" |
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28 | import="net.sf.basedb.core.SessionControl" |
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29 | import="net.sf.basedb.core.DbControl" |
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30 | import="net.sf.basedb.core.SystemItems" |
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31 | import="net.sf.basedb.core.Item" |
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32 | import="net.sf.basedb.core.ItemContext" |
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33 | import="net.sf.basedb.core.Permission" |
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34 | import="net.sf.basedb.core.AnnotationType" |
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35 | import="net.sf.basedb.core.AnnotationSet" |
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36 | import="net.sf.basedb.core.ExtendedProperties" |
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37 | import="net.sf.basedb.core.ExtendedProperty" |
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38 | import="net.sf.basedb.core.RawBioAssay" |
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39 | import="net.sf.basedb.core.Experiment" |
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40 | import="net.sf.basedb.core.RawDataType" |
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41 | import="net.sf.basedb.core.SpotImages" |
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42 | import="net.sf.basedb.core.Protocol" |
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43 | import="net.sf.basedb.core.Software" |
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44 | import="net.sf.basedb.core.ArrayDesign" |
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45 | import="net.sf.basedb.core.Job" |
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46 | import="net.sf.basedb.core.File" |
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47 | import="net.sf.basedb.core.User" |
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48 | import="net.sf.basedb.core.Group" |
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49 | import="net.sf.basedb.core.ItemQuery" |
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50 | import="net.sf.basedb.core.ItemResultIterator" |
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51 | import="net.sf.basedb.core.ItemResultList" |
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52 | import="net.sf.basedb.core.Include" |
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53 | import="net.sf.basedb.core.MultiPermissions" |
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54 | import="net.sf.basedb.core.PermissionDeniedException" |
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55 | import="net.sf.basedb.core.PluginDefinition" |
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56 | import="net.sf.basedb.core.plugin.GuiContext" |
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57 | import="net.sf.basedb.core.plugin.Plugin" |
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58 | import="net.sf.basedb.core.Project" |
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59 | import="net.sf.basedb.core.query.Orders" |
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60 | import="net.sf.basedb.core.query.Hql" |
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61 | import="net.sf.basedb.util.formatter.Formatter" |
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62 | import="net.sf.basedb.clients.web.Base" |
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63 | import="net.sf.basedb.clients.web.ChangeHistoryUtil" |
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64 | import="net.sf.basedb.clients.web.PermissionUtil" |
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65 | import="net.sf.basedb.clients.web.util.HTML" |
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66 | import="net.sf.basedb.util.Values" |
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67 | import="net.sf.basedb.util.formatter.Formatter" |
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68 | import="net.sf.basedb.clients.web.formatter.FormatterFactory" |
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69 | import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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70 | import="net.sf.basedb.clients.web.extensions.JspContext" |
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71 | import="net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer" |
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72 | import="net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil" |
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73 | import="net.sf.basedb.util.extensions.ExtensionsInvoker" |
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74 | import="java.util.Collections" |
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75 | import="java.util.Date" |
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76 | import="java.util.Map" |
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77 | import="java.util.Set" |
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78 | import="java.util.List" |
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79 | import="java.util.Date" |
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80 | %> |
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81 | <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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82 | <%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %> |
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83 | <%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %> |
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84 | <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %> |
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85 | <%@ taglib prefix="ext" uri="/WEB-INF/extensions.tld" %> |
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86 | <%! |
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87 | private static final Item itemType = Item.RAWBIOASSAY; |
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88 | private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM); |
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89 | %> |
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90 | <% |
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91 | final String root = request.getContextPath()+"/"; |
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92 | final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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93 | final String ID = sc.getId(); |
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94 | final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null); |
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95 | final int itemId = cc.getId(); |
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96 | final String tab = Values.getString(request.getParameter("tab"), "properties"); |
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97 | final float scale = Base.getScale(sc); |
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98 | final DbControl dc = sc.newDbControl(); |
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99 | try |
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100 | { |
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101 | Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext); |
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102 | |
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103 | String title = null; |
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104 | RawBioAssay rawBioAssay = RawBioAssay.getById(dc, itemId); |
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105 | RawDataType rawDataType = null; |
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106 | try |
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107 | { |
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108 | rawDataType = rawBioAssay.getRawDataType(); |
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109 | } |
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110 | catch (Throwable t) |
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111 | {} |
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112 | |
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113 | Job job = null; |
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114 | boolean readJob = true; |
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115 | try |
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116 | { |
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117 | job = rawBioAssay.getJob(); |
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118 | } |
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119 | catch (PermissionDeniedException ex) |
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120 | { |
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121 | readJob = false; |
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122 | } |
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123 | final Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc); |
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124 | Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc); |
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125 | final boolean writePermission = rawBioAssay.hasPermission(Permission.WRITE); |
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126 | final boolean deletePermission = rawBioAssay.hasPermission(Permission.DELETE); |
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127 | final boolean sharePermission = rawBioAssay.hasPermission(Permission.SET_PERMISSION); |
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128 | final boolean setOwnerPermission = rawBioAssay.hasPermission(Permission.SET_OWNER); |
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129 | final boolean isRemoved = rawBioAssay.isRemoved(); |
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130 | final boolean isUsed = isRemoved && rawBioAssay.isUsed(); |
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131 | final boolean deletePermanentlyPermission = deletePermission && !isUsed; |
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132 | final boolean isOwner = rawBioAssay.isOwner(); |
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133 | JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, guiContext, rawBioAssay); |
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134 | ExtensionsInvoker invoker = ToolbarUtil.useExtensions(jspContext); |
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135 | %> |
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136 | <base:page title="<%=title%>"> |
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137 | <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css"> |
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138 | <ext:scripts context="<%=jspContext%>" /> |
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139 | <ext:stylesheets context="<%=jspContext%>" /> |
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140 | <script language="JavaScript"> |
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141 | function editItem() |
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142 | { |
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143 | Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, true); |
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144 | } |
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145 | function shareItem() |
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146 | { |
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147 | Main.openPopup('index.jsp?ID=<%=ID%>&cmd=ShareItem&item_id=<%=itemId%>', 'ShareRawBioAssay', 600, 400); |
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148 | } |
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149 | function deleteItem() |
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150 | { |
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151 | location.replace('index.jsp?ID=<%=ID%>&cmd=DeleteItem&item_id=<%=itemId%>'); |
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152 | } |
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153 | function restoreItem() |
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154 | { |
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155 | location.replace('index.jsp?ID=<%=ID%>&cmd=RestoreItem&item_id=<%=itemId%>'); |
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156 | } |
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157 | function deleteItemPermanently() |
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158 | { |
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159 | Main.deleteItemPermanently('<%=ID%>', true, '<%=itemType.name()%>', <%=itemId%>, '&callback=itemDeleted'); |
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160 | } |
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161 | function itemDeleted() |
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162 | { |
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163 | Main.listItems('<%=ID%>', '<%=itemType.name()%>'); |
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164 | } |
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165 | function showUsingItems() |
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166 | { |
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167 | Main.showUsingItems('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>); |
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168 | } |
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169 | function setOwner() |
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170 | { |
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171 | Main.openPopup('index.jsp?ID=<%=ID%>&cmd=SetOwnerOfItem&item_id=<%=itemId%>', 'SetOwnerOfItem', 450, 300); |
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172 | } |
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173 | function runPlugin(cmd) |
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174 | { |
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175 | Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&item_id=<%=itemId%>', 'RunPlugin'+cmd, 750, 500); |
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176 | } |
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177 | function viewRawData() |
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178 | { |
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179 | location.href = 'rawdata/index.jsp?ID=<%=ID%>&cmd=List&rawbioassay_id=<%=itemId%>'; |
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180 | } |
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181 | function editSpotImages() |
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182 | { |
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183 | Main.openPopup('index.jsp?ID=<%=ID%>&cmd=EditSpotImages&item_id=<%=itemId%>', 'EditSpotImages', 600, 400); |
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184 | } |
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185 | function switchTab(tabControlId, tabId) |
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186 | { |
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187 | if (TabControl.isActive(tabControlId, tabId)) return; |
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188 | if ((tabId == 'overview' || tabId == 'history') && tabId != '<%=tab%>') |
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189 | { |
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190 | location.href = 'index.jsp?ID=<%=ID%>&cmd=ViewItem&item_id=<%=itemId%>&tab='+tabId; |
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191 | } |
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192 | else if (tabId == 'rawdata') |
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193 | { |
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194 | viewRawData(); |
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195 | } |
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196 | else |
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197 | { |
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198 | TabControl.setActiveTab(tabControlId, tabId); |
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199 | } |
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200 | } |
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201 | </script> |
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202 | </base:head> |
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203 | <base:body> |
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204 | <p:path><p:pathelement |
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205 | title="Raw bioassays" href="<%="index.jsp?ID="+ID%>" |
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206 | /><p:pathelement title="<%=HTML.encodeTags(rawBioAssay.getName())%>" |
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207 | /></p:path> |
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208 | |
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209 | <t:tabcontrol |
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210 | id="main" |
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211 | subclass="content mastertabcontrol" |
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212 | active="<%=tab%>" switch="switchTab" remember="false"> |
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213 | <t:tab id="properties" title="Properties"> |
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214 | <div> |
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215 | <table class="fullform"> |
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216 | <tr> |
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217 | <th class="itemstatus"> |
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218 | <base:icon |
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219 | image="shared.gif" |
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220 | visible="<%=rawBioAssay.isShared()%>" |
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221 | tooltip="This item is shared to other users, groups and/or projects" |
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222 | /> |
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223 | <base:icon |
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224 | image="deleted.gif" |
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225 | onclick="deleteItemPermanently()" |
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226 | tooltip="This item has been flagged for deletion. Click to delete it now." |
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227 | enabled="<%=deletePermanentlyPermission %>" |
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228 | visible="<%=isRemoved%>" |
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229 | /> |
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230 | <base:icon image="used.gif" |
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231 | onclick="showUsingItems()" |
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232 | tooltip="This item is used by other items and can't be permanently deleted. Show the items that are using this one" |
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233 | visible="<%=isRemoved && isUsed%>" /> |
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234 | </th> |
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235 | <td style="padding: 0px;"> |
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236 | <tbl:toolbar subclass="bottomborder"> |
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237 | <tbl:button |
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238 | disabled="<%=writePermission ? false : true%>" |
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239 | image="edit.gif" |
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240 | onclick="editItem()" |
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241 | title="Edit…" |
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242 | tooltip="<%=writePermission ? "Edit this raw bioassay" : "You do not have permission to edit this raw bioassay"%>" |
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243 | /> |
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244 | <tbl:button |
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245 | disabled="<%=deletePermission ? false : true%>" |
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246 | image="delete.gif" |
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247 | onclick="deleteItem()" |
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248 | title="Delete" |
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249 | visible="<%=!rawBioAssay.isRemoved()%>" |
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250 | tooltip="<%=deletePermission ? "Delete this raw bioassay" : "You do not have permission to delete this rawbioassay"%>" |
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251 | /> |
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252 | <tbl:button |
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253 | disabled="<%=writePermission ? false : true%>" |
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254 | image="restore.gif" |
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255 | onclick="restoreItem()" |
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256 | title="Restore" |
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257 | visible="<%=rawBioAssay.isRemoved()%>" |
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258 | tooltip="<%=writePermission ? "Restore this raw bioassay" : "You do not have permission to restore this rawbioassay"%>" |
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259 | /> |
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260 | <tbl:button |
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261 | disabled="<%=sharePermission ? false : true%>" |
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262 | image="share.gif" |
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263 | onclick="shareItem()" |
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264 | title="Share…" |
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265 | tooltip="<%=sharePermission ? "Share this raw bioassay to other user, groups and projects" : "You do not have permission to share this raw bioassay"%>" |
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266 | /> |
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267 | <tbl:button |
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268 | disabled="<%=setOwnerPermission ? false : true%>" |
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269 | image="take_ownership.png" |
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270 | onclick="setOwner()" |
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271 | title="Set owner…" |
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272 | tooltip="<%=setOwnerPermission ? "Change owner of this item" : "You do not have permission to change ownership of this item"%>" |
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273 | /> |
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274 | <tbl:button |
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275 | image="import.gif" |
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276 | onclick="runPlugin('ImportItem')" |
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277 | title="Import…" |
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278 | tooltip="Import data" |
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279 | visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>" |
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280 | /> |
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281 | <tbl:button |
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282 | image="export.gif" |
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283 | onclick="runPlugin('ExportItem')" |
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284 | title="Export…" |
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285 | tooltip="Export data" |
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286 | visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>" |
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287 | /> |
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288 | <tbl:button |
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289 | image="runplugin.gif" |
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290 | onclick="runPlugin('RunPlugin')" |
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291 | title="Run plugin…" |
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292 | tooltip="Run a plugin" |
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293 | visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>" |
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294 | /> |
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295 | <tbl:button |
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296 | onclick="editSpotImages()" |
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297 | image="runplugin.gif" |
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298 | title="Create spot images…" |
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299 | visible="<%=writePermission && rawBioAssay.getNumDbSpots() > 0%>" |
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300 | /> |
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301 | <ext:render extensions="<%=invoker%>" context="<%=jspContext%>" |
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302 | wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/> |
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303 | <tbl:button |
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304 | image="help.png" |
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305 | onclick="<%="Main.openHelp('" + ID +"', 'rawbioassay.view.properties')"%>" |
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306 | title="Help…" |
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307 | tooltip="Get help about this page" |
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308 | /> |
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309 | </tbl:toolbar> |
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310 | </td> |
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311 | </tr> |
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312 | </table> |
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313 | <table style="width: 100%; height: 20em;" class="bottomborder"> |
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314 | <tr valign="top"> |
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315 | <td style="width: 50%; height: 100%;"> |
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316 | <table class="fullform" > |
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317 | <tr> |
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318 | <th>Name</th> |
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319 | <td><%=HTML.encodeTags(rawBioAssay.getName())%></td> |
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320 | </tr> |
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321 | <tr> |
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322 | <th>Registered</th> |
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323 | <td><%=dateFormatter.format(rawBioAssay.getEntryDate())%></td> |
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324 | </tr> |
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325 | <tr> |
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326 | <th>Platform</th> |
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327 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="platform" /></td> |
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328 | </tr> |
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329 | <tr> |
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330 | <th>Variant</th> |
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331 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="variant" /></td> |
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332 | </tr> |
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333 | <tr> |
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334 | <th>Raw data type</th> |
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335 | <td><base:catch><%=HTML.encodeTags(rawBioAssay.getRawDataType().getName())%></base:catch></td> |
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336 | </tr> |
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337 | <tr> |
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338 | <th>Spots</th> |
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339 | <td><%=rawBioAssay.hasData() ? "yes (db: " + rawBioAssay.getNumDbSpots() + |
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340 | "; file: " + rawBioAssay.getNumFileSpots() + ")" : "no"%></td> |
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341 | </tr> |
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342 | <tr> |
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343 | <th>Parent bioassay</th> |
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344 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="parentBioAssay" /></td> |
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345 | </tr> |
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346 | <tr> |
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347 | <th>Parent extract</th> |
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348 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="parentExtract" /></td> |
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349 | </tr> |
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350 | <tr> |
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351 | <th>Protocol</th> |
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352 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="protocol" /></td> |
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353 | </tr> |
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354 | <tr> |
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355 | <th>Software</th> |
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356 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="software" /></td> |
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357 | </tr> |
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358 | <tr> |
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359 | <th>Array design</th> |
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360 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="arrayDesign" /></td> |
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361 | </tr> |
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362 | <tr> |
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363 | <th>Owner</th> |
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364 | <td><base:propertyvalue item="<%=rawBioAssay%>" property="owner" /></td> |
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365 | </tr> |
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366 | <tr class="dynamic"> |
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367 | <th>Description</th> |
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368 | <td><%=HTML.niceFormat(rawBioAssay.getDescription())%></td> |
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369 | </tr> |
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370 | </table> |
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371 | </td> |
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372 | <td style="width: 50%; height: 100%;" class="leftborder"> |
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373 | <table class="fullform"> |
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374 | <tbody class="sectionheader"> |
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375 | <tr> |
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376 | <th colspan="4">Raw data import</th> |
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377 | </tr> |
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378 | </tbody> |
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379 | <tr> |
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380 | <th>Job</th> |
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381 | <td colspan="3"><%=Base.getLinkedName(ID, job, !readJob, true)%></td> |
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382 | </tr> |
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383 | <tr> |
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384 | <th>Date / time</th> |
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385 | <td colspan="3"><%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%></td> |
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386 | </tr> |
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387 | <tr> |
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388 | <th>Plugin</th> |
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389 | <td colspan="3"><base:propertyvalue item="<%=rawBioAssay%>" property="job.pluginDefinition" /></td> |
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390 | </tr> |
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391 | <tr> |
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392 | <th>Configuration / file format</th> |
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393 | <td colspan="3"><base:propertyvalue item="<%=rawBioAssay%>" property="job.pluginConfiguration" /></td> |
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394 | </tr> |
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395 | <tbody class="sectionheader"> |
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396 | <tr> |
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397 | <th colspan="4">Spot images</th> |
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398 | </tr> |
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399 | </tbody> |
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400 | <% |
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401 | if (!rawBioAssay.hasSpotImages()) |
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402 | { |
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403 | %> |
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404 | <tr class="dynamic"> |
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405 | <td colspan="4"> |
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406 | <div class="messagecontainer note"> |
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407 | No spot images has been created for this raw bioassay. |
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408 | </div> |
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409 | </td> |
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410 | </tr> |
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411 | <% |
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412 | } |
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413 | else |
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414 | { |
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415 | SpotImages spi = rawBioAssay.getSpotImages(); |
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416 | %> |
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417 | <tr> |
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418 | <th>X scale</th> |
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419 | <td><%=spi.getXScale()%></td> |
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420 | <th class="leftborder">Spot size</th> |
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421 | <td><%=spi.getSpotsize()%></td> |
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422 | </tr> |
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423 | <tr> |
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424 | <th>Y scale</th> |
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425 | <td><%=spi.getYScale()%></td> |
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426 | <th class="leftborder">Gamma correction</th> |
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427 | <td><%=spi.getGamma()%></td> |
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428 | </tr> |
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429 | <tr> |
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430 | <th>X offset</th> |
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431 | <td><%=spi.getXOffset()%></td> |
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432 | <th class="leftborder">Quality</th> |
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433 | <td><%=spi.getQuality()%></td> |
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434 | </tr> |
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435 | <tr> |
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436 | <th>Y offset</th> |
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437 | <td><%=spi.getYOffset()%></td> |
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438 | <th class="leftborder"></th> |
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439 | <td></td> |
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440 | </tr> |
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441 | <tr> |
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442 | <th class="topborder">Red image file</th> |
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443 | <td colspan="3" class="topborder"><base:propertyvalue item="<%=spi%>" property="redImageFile" /></td> |
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444 | </tr> |
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445 | <tr> |
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446 | <th>Green image file</th> |
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447 | <td colspan="3"><base:propertyvalue item="<%=spi%>" property="greenImageFile" /></td> |
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448 | </tr> |
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449 | <tr> |
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450 | <th>Blue image file</th> |
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451 | <td colspan="3"><base:propertyvalue item="<%=spi%>" property="blueImageFile" /></td> |
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452 | </tr> |
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453 | <tr> |
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454 | <th>Spot images file</th> |
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455 | <td colspan="3"><base:propertyvalue item="<%=spi%>" property="spotImagesFile" /></td> |
---|
456 | </tr> |
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457 | <% |
---|
458 | } |
---|
459 | %> |
---|
460 | </table> |
---|
461 | </td> |
---|
462 | </tr> |
---|
463 | </table> |
---|
464 | </div> |
---|
465 | |
---|
466 | <jsp:include page="../../common/datafiles/list_files.jsp"> |
---|
467 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
468 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
469 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
470 | </jsp:include> |
---|
471 | |
---|
472 | <% |
---|
473 | Set<String> names = rawBioAssay.getHeaderNames(); |
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474 | %> |
---|
475 | <base:section |
---|
476 | id="headers" |
---|
477 | title="<%="Raw data headers (" + (names == null ? 0 : names.size()) + ")"%>" |
---|
478 | context="<%=cc%>" |
---|
479 | > |
---|
480 | <% |
---|
481 | if (names == null || names.size() == 0) |
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482 | { |
---|
483 | %> |
---|
484 | <div class="messagecontainer note"> |
---|
485 | None. |
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486 | </div> |
---|
487 | <% |
---|
488 | } |
---|
489 | else |
---|
490 | { |
---|
491 | %> |
---|
492 | <table class="fullform fullborder"> |
---|
493 | <% |
---|
494 | boolean needsTr = true; |
---|
495 | if (names != null) |
---|
496 | { |
---|
497 | for (String name : names) |
---|
498 | { |
---|
499 | %> |
---|
500 | <%=needsTr ? "<tr><th>" : "<th class=\"leftborder\">" %> |
---|
501 | <%=HTML.encodeTags(name)%></th> |
---|
502 | <td><%=HTML.encodeTags(rawBioAssay.getHeader(name))%></td> |
---|
503 | <%=needsTr ? "" : "</tr>"%> |
---|
504 | <% |
---|
505 | needsTr = !needsTr; |
---|
506 | } |
---|
507 | %> |
---|
508 | <%=needsTr ? "" : "<th class=\"leftborder\"></th><td></td></tr>"%> |
---|
509 | <% |
---|
510 | } |
---|
511 | %> |
---|
512 | </table> |
---|
513 | <% |
---|
514 | } |
---|
515 | %> |
---|
516 | </base:section> |
---|
517 | <% |
---|
518 | ItemQuery<Experiment> experimentQuery = rawBioAssay.getExperiments(); |
---|
519 | experimentQuery.include(Include.ALL); |
---|
520 | experimentQuery.order(Orders.asc(Hql.property("name"))); |
---|
521 | ItemResultList<Experiment> experiments = experimentQuery.list(dc); |
---|
522 | %> |
---|
523 | <base:section |
---|
524 | id="experiments" |
---|
525 | title="<%="Experiments (" + experiments.size() + ")"%>" |
---|
526 | context="<%=cc%>" |
---|
527 | > |
---|
528 | <% |
---|
529 | if (experiments.size() == 0) |
---|
530 | { |
---|
531 | %> |
---|
532 | <div class="messagecontainer note"> |
---|
533 | This raw bioassay isn't used in any experiments |
---|
534 | (or, you don't have permission to view them). |
---|
535 | </div> |
---|
536 | <% |
---|
537 | } |
---|
538 | else |
---|
539 | { |
---|
540 | %> |
---|
541 | <tbl:table |
---|
542 | id="experiments" |
---|
543 | columns="all" |
---|
544 | > |
---|
545 | <tbl:columndef |
---|
546 | id="name" |
---|
547 | title="Name" |
---|
548 | /> |
---|
549 | <tbl:columndef |
---|
550 | id="description" |
---|
551 | title="Description" |
---|
552 | /> |
---|
553 | <tbl:data> |
---|
554 | <tbl:headers> |
---|
555 | <tbl:headerrow> |
---|
556 | <tbl:columnheaders /> |
---|
557 | </tbl:headerrow> |
---|
558 | </tbl:headers> |
---|
559 | <tbl:rows> |
---|
560 | <% |
---|
561 | for (Experiment item : experiments) |
---|
562 | { |
---|
563 | %> |
---|
564 | <tbl:row> |
---|
565 | <tbl:cell column="name"><base:icon |
---|
566 | image="deleted.gif" |
---|
567 | tooltip="This item has been scheduled for deletion" |
---|
568 | visible="<%=item.isRemoved()%>" |
---|
569 | /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell> |
---|
570 | <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell> |
---|
571 | </tbl:row> |
---|
572 | <% |
---|
573 | } |
---|
574 | %> |
---|
575 | </tbl:rows> |
---|
576 | </tbl:data> |
---|
577 | </tbl:table> |
---|
578 | <% |
---|
579 | } |
---|
580 | %> |
---|
581 | </base:section> |
---|
582 | |
---|
583 | <jsp:include page="../../common/anytoany/list_anytoany.jsp"> |
---|
584 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
585 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
586 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
587 | <jsp:param name="title" value="Other items related to this sample" /> |
---|
588 | </jsp:include> |
---|
589 | <jsp:include page="../../common/share/list_share.jsp"> |
---|
590 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
591 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
592 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
593 | <jsp:param name="title" value="Shared to" /> |
---|
594 | </jsp:include> |
---|
595 | </t:tab> |
---|
596 | |
---|
597 | <t:tab id="annotations" title="Annotations & parameters" |
---|
598 | tooltip="View annotation values and protocol parameters" clazz="white"> |
---|
599 | <jsp:include page="../../common/annotations/list_annotations.jsp"> |
---|
600 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
601 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
602 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
603 | </jsp:include> |
---|
604 | </t:tab> |
---|
605 | |
---|
606 | <t:tab id="rawdata" title="Raw data" visible="<%=rawBioAssay.getNumDbSpots() > 0%>" /> |
---|
607 | <t:tab id="overview" title="Overview" |
---|
608 | tooltip="Display a tree overview of related items"> |
---|
609 | <% |
---|
610 | if ("overview".equals(tab)) |
---|
611 | { |
---|
612 | %> |
---|
613 | <jsp:include page="../../common/overview/overview.jsp"> |
---|
614 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
615 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
616 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
617 | </jsp:include> |
---|
618 | <% |
---|
619 | } |
---|
620 | %> |
---|
621 | </t:tab> |
---|
622 | <t:tab id="history" title="Change history" |
---|
623 | tooltip="Displays a log of all modifications made to this item" |
---|
624 | visible="<%=ChangeHistoryUtil.showChangeHistoryTab(sc)%>"> |
---|
625 | <% |
---|
626 | if ("history".equals(tab)) |
---|
627 | { |
---|
628 | %> |
---|
629 | <jsp:include page="../../common/history/frameset.jsp"> |
---|
630 | <jsp:param name="source_type" value="<%=itemType.name()%>" /> |
---|
631 | <jsp:param name="source_id" value="<%=itemId%>" /> |
---|
632 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
633 | </jsp:include> |
---|
634 | <% |
---|
635 | } |
---|
636 | %> |
---|
637 | </t:tab> |
---|
638 | </t:tabcontrol> |
---|
639 | |
---|
640 | </base:body> |
---|
641 | </base:page> |
---|
642 | <% |
---|
643 | } |
---|
644 | finally |
---|
645 | { |
---|
646 | if (dc != null) dc.close(); |
---|
647 | } |
---|
648 | |
---|
649 | %> |
---|