1 | <%-- $Id: view_bioassayset.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 Johan Enell |
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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 | import="net.sf.basedb.core.SessionControl" |
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28 | import="net.sf.basedb.core.DbControl" |
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29 | import="net.sf.basedb.core.Item" |
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30 | import="net.sf.basedb.core.ItemContext" |
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31 | import="net.sf.basedb.core.Permission" |
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32 | import="net.sf.basedb.core.Experiment" |
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33 | import="net.sf.basedb.core.BioAssaySet" |
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34 | import="net.sf.basedb.core.BioAssay" |
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35 | import="net.sf.basedb.core.Transformation" |
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36 | import="net.sf.basedb.core.Job" |
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37 | import="net.sf.basedb.core.PluginDefinition" |
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38 | import="net.sf.basedb.core.PluginConfiguration" |
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39 | import="net.sf.basedb.core.User" |
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40 | import="net.sf.basedb.core.ItemQuery" |
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41 | import="net.sf.basedb.core.ItemResultList" |
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42 | import="net.sf.basedb.core.Include" |
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43 | import="net.sf.basedb.core.PermissionDeniedException" |
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44 | import="net.sf.basedb.core.PluginDefinition" |
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45 | import="net.sf.basedb.core.ParameterInfo" |
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46 | import="net.sf.basedb.core.RawDataType" |
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47 | import="net.sf.basedb.core.BasicItem" |
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48 | import="net.sf.basedb.core.Nameable" |
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49 | import="net.sf.basedb.core.File" |
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50 | import="net.sf.basedb.core.plugin.GuiContext" |
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51 | import="net.sf.basedb.core.plugin.Plugin" |
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52 | import="net.sf.basedb.core.query.Orders" |
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53 | import="net.sf.basedb.core.query.Hql" |
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54 | import="net.sf.basedb.clients.web.Base" |
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55 | import="net.sf.basedb.clients.web.PermissionUtil" |
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56 | import="net.sf.basedb.clients.web.util.HTML" |
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57 | import="net.sf.basedb.util.Values" |
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58 | import="net.sf.basedb.util.formatter.Formatter" |
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59 | import="net.sf.basedb.clients.web.formatter.FormatterFactory" |
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60 | import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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61 | import="net.sf.basedb.clients.web.extensions.JspContext" |
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62 | import="net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer" |
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63 | import="net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil" |
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64 | import="net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction" |
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65 | import="net.sf.basedb.clients.web.extensions.plot.PlotGenerator" |
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66 | import="net.sf.basedb.util.extensions.ExtensionsInvoker" |
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67 | import="net.sf.basedb.util.extensions.ActionIterator" |
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68 | import="java.util.Date" |
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69 | import="java.util.Map" |
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70 | import="java.util.Set" |
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71 | import="java.util.List" |
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72 | import="java.util.Iterator" |
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73 | %> |
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74 | <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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75 | <%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %> |
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76 | <%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %> |
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77 | <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %> |
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78 | <%@ taglib prefix="ext" uri="/WEB-INF/extensions.tld" %> |
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79 | <%! |
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80 | private static final Item itemType = Item.BIOASSAYSET; |
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81 | private static final GuiContext guiContext = new GuiContext(itemType, GuiContext.Type.ITEM); |
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82 | %> |
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83 | <% |
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84 | final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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85 | final String ID = sc.getId(); |
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86 | final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null); |
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87 | final int itemId = cc.getId(); |
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88 | final String tabId = Values.getString(request.getParameter("tab"), "properties"); |
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89 | |
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90 | final float scale = Base.getScale(sc); |
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91 | final String root = request.getContextPath(); |
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92 | final DbControl dc = sc.newDbControl(); |
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93 | try |
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94 | { |
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95 | Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext); |
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96 | |
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97 | String title = null; |
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98 | final BioAssaySet bioAssaySet = BioAssaySet.getById(dc, itemId); |
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99 | final Experiment experiment = bioAssaySet.getExperiment(); |
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100 | final int experimentId = experiment.getId(); |
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101 | final boolean hasDbSpots = bioAssaySet.getNumSpots() > 0; |
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102 | Transformation transformation = bioAssaySet.getTransformation(); |
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103 | RawDataType rawDataType = experiment.getRawDataType(); |
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104 | |
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105 | Job job = null; |
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106 | boolean readJob = true; |
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107 | PluginDefinition plugin = null; |
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108 | boolean readPlugin = true; |
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109 | PluginConfiguration configuration = null; |
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110 | boolean readConfiguration = true; |
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111 | |
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112 | try |
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113 | { |
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114 | job = transformation.getJob(); |
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115 | } |
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116 | catch (PermissionDeniedException ex) |
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117 | { |
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118 | readJob = false; |
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119 | readPlugin = false; |
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120 | readConfiguration = false; |
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121 | } |
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122 | if (job != null) |
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123 | { |
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124 | try |
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125 | { |
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126 | plugin = job.getPluginDefinition(); |
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127 | } |
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128 | catch (PermissionDeniedException ex) |
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129 | { |
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130 | readPlugin = false; |
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131 | } |
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132 | try |
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133 | { |
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134 | configuration = job.getPluginConfiguration(); |
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135 | } |
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136 | catch (PermissionDeniedException ex) |
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137 | { |
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138 | readConfiguration = false; |
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139 | } |
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140 | } |
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141 | |
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142 | final boolean createPermission = experiment.hasPermission(Permission.USE); |
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143 | final boolean writePermission = bioAssaySet.hasPermission(Permission.WRITE); |
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144 | final boolean deletePermission = bioAssaySet.hasPermission(Permission.DELETE); |
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145 | Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc); |
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146 | Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc); |
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147 | JspContext jspContext = ExtensionsControl.createContext(dc, pageContext, guiContext, bioAssaySet); |
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148 | ExtensionsInvoker toolbarInvoker = ToolbarUtil.useExtensions(jspContext); |
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149 | ExtensionsInvoker overviewPlotInvoker = ExtensionsControl.useExtensions(jspContext, |
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150 | "net.sf.basedb.clients.web.bioassayset.overviewplots"); |
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151 | %> |
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152 | <base:page title="<%=title%>"> |
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153 | <base:head scripts="table.js,tabcontrol.js,newjoust.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css,newjoust.css"> |
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154 | <ext:scripts context="<%=jspContext%>" /> |
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155 | <ext:stylesheets context="<%=jspContext%>" /> |
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156 | <script language="JavaScript"> |
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157 | function editItem() |
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158 | { |
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159 | Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, true); |
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160 | } |
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161 | function deleteItem() |
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162 | { |
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163 | location.replace('index.jsp?ID=<%=ID%>&cmd=DeleteItem&experiment_id=<%=experimentId%>&item_id=<%=itemId%>'); |
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164 | } |
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165 | function restoreItem() |
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166 | { |
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167 | location.replace('index.jsp?ID=<%=ID%>&cmd=RestoreItem&experiment_id=<%=experimentId%>&item_id=<%=itemId%>'); |
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168 | } |
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169 | function switchTab(tabControlId, tabId) |
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170 | { |
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171 | if (TabControl.isActive(tabControlId, tabId)) return; |
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172 | if (tabId == 'bioassays') |
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173 | { |
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174 | location.href = '../bioassays/index.jsp?ID=<%=ID%>&experiment_id=<%=experimentId%>&bioassayset_id=<%=itemId%>&tab='+tabId; |
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175 | } |
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176 | else if (tabId == 'spotdata') |
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177 | { |
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178 | location.href = '../spotdata/index.jsp?ID=<%=ID%>&experiment_id=<%=experimentId%>&bioassayset_id=<%=itemId%>'; |
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179 | } |
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180 | else if ((tabId == 'overviewplots' || tabId == 'cfplots') && tabId != '<%=tabId%>') |
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181 | { |
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182 | location.href = 'index.jsp?ID=<%=ID%>&cmd=ViewItem&experiment_id=<%=experimentId%>&bioassayset_id=<%=itemId%>&tab='+tabId; |
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183 | } |
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184 | else |
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185 | { |
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186 | TabControl.setActiveTab(tabControlId, tabId); |
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187 | } |
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188 | } |
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189 | function runItemPlugin(cmd) |
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190 | { |
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191 | Main.openPopup('index.jsp?ID=<%=ID%>&cmd='+cmd+'&experiment_id=<%=experimentId%>&item_id=<%=itemId%>', 'RunPlugin'+cmd, 750, 500); |
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192 | } |
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193 | |
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194 | function ImageQueue(baseId) |
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195 | { |
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196 | this.images = new Array(); |
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197 | this.nextImage = 0; |
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198 | |
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199 | this.addImage = function(imageId, url) |
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200 | { |
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201 | this.images[this.images.length] = imageId; |
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202 | var img = document.getElementById(imageId); |
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203 | img.realSrc = url; |
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204 | } |
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205 | |
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206 | this.loadNextImage = function() |
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207 | { |
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208 | if (this.images.length <= this.nextImage) return; |
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209 | var imageId = this.images[this.nextImage]; |
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210 | var img = document.getElementById(imageId); |
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211 | img.src = '../../../images/plot_generating_400x300.gif'; |
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212 | img.realImg = new Image(); |
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213 | img.realImg.onload = function() |
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214 | { |
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215 | img.src = img.realImg.src; |
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216 | img.style.background = 'transparent'; |
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217 | setTimeout('loadNextImage()', 100); |
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218 | }; |
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219 | img.realImg.src = img.realSrc; |
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220 | this.nextImage++; |
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221 | } |
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222 | } |
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223 | |
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224 | var plotQueue = new Array(); |
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225 | var currentQueue = null; |
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226 | function registerImage(baseId, plotId, url) |
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227 | { |
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228 | if (!currentQueue) currentQueue = baseId; |
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229 | var imageQueue = plotQueue[baseId]; |
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230 | if (!imageQueue) |
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231 | { |
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232 | imageQueue = new ImageQueue(baseId); |
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233 | plotQueue[baseId] = imageQueue; |
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234 | } |
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235 | var imageId = baseId + '.' + plotId; |
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236 | imageQueue.addImage(imageId, url); |
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237 | } |
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238 | function switchOverview(tabControlId, tabId) |
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239 | { |
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240 | currentQueue = tabId; |
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241 | TabControl.setActiveTab(tabControlId, tabId); |
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242 | loadNextImage(); |
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243 | } |
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244 | function loadNextImage() |
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245 | { |
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246 | var imageQueue = plotQueue[currentQueue]; |
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247 | if (imageQueue) imageQueue.loadNextImage(); |
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248 | } |
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249 | </script> |
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250 | <style> |
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251 | .plot |
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252 | { |
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253 | border: 1px solid #A0A0A0; |
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254 | background-image: url('../../../images/plot_empty_400x300.png'); |
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255 | margin: 2px; |
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256 | } |
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257 | </style> |
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258 | </base:head> |
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259 | <base:body onload="loadNextImage()"> |
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260 | <p:path><p:pathelement |
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261 | title="Experiments" href="<%="../index.jsp?ID="+ID%>" |
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262 | /><p:pathelement title="<%=HTML.encodeTags(experiment.getName())%>" |
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263 | href="<%="index.jsp?ID="+ID+"&experiment_id="+experimentId%>" |
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264 | /><p:pathelement title="<%=HTML.encodeTags(bioAssaySet.getName())%>" |
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265 | /></p:path> |
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266 | |
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267 | <t:tabcontrol |
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268 | id="view" |
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269 | subclass="content mastertabcontrol" |
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270 | active="<%=tabId%>" switch="switchTab" remember="false"> |
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271 | <t:tab id="properties" title="Properties"> |
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272 | <div> |
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273 | <table class="fullform"> |
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274 | <tr> |
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275 | <th class="itemstatus"> |
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276 | <base:icon |
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277 | image="deleted.gif" |
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278 | onclick="deleteItemPermanently()" |
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279 | tooltip="This item has been flagged for deletion. Click to delete it now." |
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280 | enabled="<%=deletePermission %>" |
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281 | visible="<%=bioAssaySet.isRemoved()%>" |
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282 | /> |
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283 | </th> |
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284 | <td style="padding: 0px;" colspan="2"> |
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285 | <tbl:toolbar subclass="bottomborder"> |
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286 | <tbl:button |
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287 | disabled="<%=writePermission ? false : true%>" |
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288 | image="edit.gif" |
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289 | onclick="editItem()" |
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290 | title="Edit…" |
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291 | tooltip="<%=writePermission ? "Edit this bioassay set" : "You do not have permission to edit this bioassay set"%>" |
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292 | /> |
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293 | <tbl:button |
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294 | disabled="<%=deletePermission ? false : true%>" |
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295 | image="delete.gif" |
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296 | onclick="deleteItem()" |
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297 | title="Delete" |
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298 | visible="<%=!bioAssaySet.isRemoved()%>" |
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299 | tooltip="<%=deletePermission ? "Delete this bioassay set" : "You do not have permission to delete this bioassay set"%>" |
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300 | /> |
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301 | <tbl:button |
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302 | disabled="<%=writePermission ? false : true%>" |
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303 | image="restore.gif" |
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304 | onclick="restoreItem()" |
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305 | title="Restore" |
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306 | visible="<%=bioAssaySet.isRemoved()%>" |
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307 | tooltip="<%=writePermission ? "Restore this bioassay set" : "You do not have permission to restore this bioassay set"%>" |
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308 | /> |
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309 | <tbl:button |
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310 | image="import.gif" |
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311 | onclick="runItemPlugin('ImportItem')" |
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312 | title="Import…" |
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313 | tooltip="Import data" |
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314 | visible="<%=pluginCount.containsKey(Plugin.MainType.IMPORT)%>" |
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315 | /> |
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316 | <tbl:button |
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317 | image="export.gif" |
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318 | onclick="runItemPlugin('ExportItem')" |
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319 | title="Export…" |
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320 | tooltip="Export data" |
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321 | visible="<%=pluginCount.containsKey(Plugin.MainType.EXPORT)%>" |
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322 | /> |
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323 | <tbl:button |
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324 | image="plotter.gif" |
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325 | onclick="<%="openPlotTool(" + itemId + ")"%>" |
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326 | title="Plot tool…" |
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327 | tooltip="A simple tool for generating plots" |
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328 | visible="<%=hasDbSpots%>" |
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329 | /> |
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330 | <tbl:button |
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331 | image="explorer.png" |
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332 | onclick="<%="openExperimentExplorer(" + itemId + ")"%>" |
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333 | title="Experiment explorer" |
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334 | tooltip="View the data reporter by reporter" |
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335 | visible="<%=hasDbSpots%>" |
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336 | /> |
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337 | <tbl:button |
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338 | disabled="<%=!createPermission%>" |
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339 | image="filter.gif" |
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340 | onclick="<%="filter(" + itemId +")"%>" |
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341 | title="Filter bioassay set…" |
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342 | tooltip="<%=createPermission ? |
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343 | "Create a new bioassay set by filtering this bioassayset" : |
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344 | "You do not have permission analyze this experiment"%>" |
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345 | visible="<%=pluginCount.containsKey(Plugin.MainType.ANALYZE)%>" |
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346 | /> |
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347 | <tbl:button |
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348 | image="runplugin.gif" |
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349 | onclick="runItemPlugin('RunPlugin')" |
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350 | title="Run plugin…" |
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351 | tooltip="Run a plugin" |
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352 | visible="<%=pluginCount.containsKey(Plugin.MainType.OTHER)%>" |
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353 | /> |
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354 | <tbl:button |
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355 | disabled="<%=!createPermission%>" |
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356 | image="<%=createPermission ? "runplugin.gif" : "runplugin_disabled.gif"%>" |
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357 | onclick="<%="runAnalysisPlugin(" + itemId + ")"%>" |
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358 | title="Run analysis…" |
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359 | tooltip="<%=createPermission ? "Run an analysis plugin" : |
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360 | "You do not have permission to analyze this experiment"%>" |
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361 | visible="<%=pluginCount.containsKey(Plugin.MainType.ANALYZE)%>" |
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362 | /> |
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363 | <ext:render extensions="<%=toolbarInvoker%>" context="<%=jspContext%>" |
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364 | wrapper="<%=new PrefixSuffixRenderer(jspContext, "<td>", "</td>") %>"/> |
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365 | <tbl:button |
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366 | image="help.png" |
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367 | onclick="<%="Main.openHelp('" + ID +"', 'bioassayset.view.properties')"%>" |
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368 | title="Help…" |
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369 | tooltip="Get help about this page" |
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370 | /> |
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371 | </tbl:toolbar> |
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372 | </td> |
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373 | </tr> |
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374 | </table> |
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375 | <table style="width: 100%; height: 16em;" class="bottomborder"> |
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376 | <tr valign="top"> |
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377 | <td style="width: 50%; height: 100%;"> |
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378 | <table class="fullform" > |
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379 | <tr> |
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380 | <th>Name</th> |
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381 | <td><%=HTML.encodeTags(bioAssaySet.getName())%></td> |
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382 | </tr> |
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383 | <tr> |
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384 | <th>Experiment</th> |
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385 | <td><%=Base.getLinkedName(ID, experiment, false, writePermission)%> |
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386 | (<%=experiment.getRawDataType()%>)</td> |
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387 | </tr> |
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388 | <tr> |
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389 | <th>Intensity transformation</th> |
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390 | <td><%=bioAssaySet.getIntensityTransform().toString()%></td> |
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391 | </tr> |
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392 | <tr> |
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393 | <th>Spots</th> |
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394 | <td>db: <%=bioAssaySet.getNumSpots()%>; file: <%=bioAssaySet.getNumFileSpots()%></td> |
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395 | </tr> |
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396 | <tr> |
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397 | <th>Reporters</th> |
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398 | <td>db: <%=bioAssaySet.getNumReporters()%>; file: <%=bioAssaySet.getNumFileReporters()%></td> |
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399 | </tr> |
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400 | <tr> |
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401 | <th>Permissions</th> |
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402 | <td><%=PermissionUtil.getFullPermissionNames(bioAssaySet)%></td> |
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403 | </tr> |
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404 | <tr> |
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405 | <th>Description</th> |
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406 | <td><%=HTML.niceFormat(bioAssaySet.getDescription())%></td> |
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407 | </tr> |
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408 | <tbody class="sectionheader"> |
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409 | <tr> |
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410 | <th colspan="2">Transformation & job</th> |
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411 | </tr> |
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412 | </tbody> |
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413 | <tr> |
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414 | <th>Transformation</th> |
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415 | <td><%=Base.getLinkedName(ID, transformation, false, |
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416 | transformation.hasPermission(Permission.WRITE))%></td> |
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417 | </tr> |
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418 | <tr> |
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419 | <th>Job</th> |
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420 | <td><%=Base.getLinkedName(ID, job, !readJob, false)%></td> |
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421 | </tr> |
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422 | <tr > |
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423 | <th>Started</th> |
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424 | <td> |
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425 | <%=job == null ? "" : dateTimeFormatter.format(job.getStarted())%> |
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426 | </td> |
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427 | </tr> |
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428 | <tr> |
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429 | <th>Ended</th> |
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430 | <td> |
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431 | <%=job == null ? "" : dateTimeFormatter.format(job.getEnded())%> |
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432 | </td> |
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433 | </tr> |
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434 | <tr> |
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435 | <th>Server</th> |
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436 | <td> |
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437 | <%=job == null ? "" : HTML.encodeTags(job.getServer())%> |
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438 | </td> |
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439 | </tr> |
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440 | <tr> |
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441 | <th>Description</th> |
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442 | <td><%=HTML.niceFormat(transformation.getDescription())%></td> |
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443 | </tr> |
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444 | </table> |
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445 | </td> |
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446 | <td style="width: 50%;" class="leftborder"> |
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447 | <table class="fullform" > |
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448 | <tbody class="sectionheader"> |
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449 | <tr> |
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450 | <th colspan="2">Plugin & parameters</th> |
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451 | </tr> |
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452 | </tbody> |
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453 | <tr> |
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454 | <th>Plugin</th> |
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455 | <td><%=Base.getLinkedName(ID, plugin, |
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456 | !readPlugin, plugin != null && plugin.hasPermission(Permission.WRITE))%></td> |
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457 | </tr> |
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458 | <tr> |
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459 | <th>Plugin configuration</th> |
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460 | <td><%=Base.getLinkedName(ID, configuration, !readConfiguration, |
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461 | configuration != null && configuration.hasPermission(Permission.WRITE))%></td> |
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462 | </tr> |
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463 | <% |
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464 | if (job != null) |
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465 | { |
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466 | for (String name : job.getParameterNames()) |
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467 | { |
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468 | StringBuilder sb = new StringBuilder(); |
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469 | String displayValue = ""; |
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470 | String description = ""; |
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471 | try |
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472 | { |
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473 | ParameterInfo pi = job.getParameterInfo(name); |
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474 | if (pi.getLabel() != null) name = HTML.encodeTags(pi.getLabel()); |
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475 | description = HTML.encodeTags(pi.getDescription()); |
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476 | List<?> values = pi.getValues(); |
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477 | int i = 0; |
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478 | for (Object value : values) |
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479 | { |
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480 | if (value != null) |
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481 | { |
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482 | if (i > 0) sb.append(", "); |
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483 | i++; |
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484 | if (value instanceof BasicItem) |
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485 | { |
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486 | BasicItem item = (BasicItem)value; |
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487 | String itemName = ""; |
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488 | if (item instanceof File) |
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489 | { |
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490 | itemName = ((File)item).getPath().toString(); |
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491 | } |
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492 | else if (item instanceof Nameable) |
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493 | { |
---|
494 | itemName = ((Nameable)item).getName(); |
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495 | } |
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496 | else |
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497 | { |
---|
498 | itemName = item.toString(); |
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499 | } |
---|
500 | sb.append(Base.getLink(ID, HTML.encodeTags(itemName), |
---|
501 | item.getType(), item.getId(), item.hasPermission(Permission.WRITE))); |
---|
502 | } |
---|
503 | else if (value instanceof Date) |
---|
504 | { |
---|
505 | sb.append(dateFormatter.format((Date)value)); |
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506 | } |
---|
507 | else |
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508 | { |
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509 | sb.append(HTML.encodeTags(value.toString())); |
---|
510 | } |
---|
511 | } |
---|
512 | } |
---|
513 | displayValue = sb.toString(); |
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514 | } |
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515 | catch (Throwable ex) |
---|
516 | { |
---|
517 | displayValue = "<i>ERROR: "+ex.getMessage()+"</i>"; |
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518 | } |
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519 | %> |
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520 | <tr> |
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521 | <th><span title="<%=description%>"><%=name%></span></th> |
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522 | <td> |
---|
523 | <%=displayValue%> |
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524 | </td> |
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525 | </tr> |
---|
526 | <% |
---|
527 | } |
---|
528 | } |
---|
529 | %> |
---|
530 | <tr class="dynamic"> |
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531 | <th></th> |
---|
532 | <td></td> |
---|
533 | </tr> |
---|
534 | </table> |
---|
535 | |
---|
536 | </td> |
---|
537 | </tr> |
---|
538 | </table> |
---|
539 | </div> |
---|
540 | <jsp:include page="../../../common/datafiles/list_files.jsp"> |
---|
541 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
542 | <jsp:param name="item_id" value="<%=itemId%>" /> |
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543 | <jsp:param name="ID" value="<%=ID%>" /> |
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544 | </jsp:include> |
---|
545 | |
---|
546 | <jsp:include page="../../../common/anytoany/list_anytoany.jsp"> |
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547 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
548 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
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549 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
550 | <jsp:param name="title" value="Other items related to this bioassay set" /> |
---|
551 | </jsp:include> |
---|
552 | |
---|
553 | <base:section id="anaysis" title="Analysis subtree" context="<%=cc%>"> |
---|
554 | <jsp:include page="analysis_tree.jsp"> |
---|
555 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
556 | <jsp:param name="experiment_id" value="<%=experimentId%>" /> |
---|
557 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
558 | </jsp:include> |
---|
559 | </base:section> |
---|
560 | </t:tab> |
---|
561 | |
---|
562 | <t:tab id="annotations" title="Annotations" |
---|
563 | tooltip="View annotation values" clazz="white"> |
---|
564 | <jsp:include page="../../../common/annotations/list_annotations.jsp"> |
---|
565 | <jsp:param name="item_type" value="<%=itemType.name()%>" /> |
---|
566 | <jsp:param name="item_id" value="<%=itemId%>" /> |
---|
567 | <jsp:param name="ID" value="<%=ID%>" /> |
---|
568 | </jsp:include> |
---|
569 | </t:tab> |
---|
570 | |
---|
571 | <t:tab id="bioassays" title="Bioassays" /> |
---|
572 | |
---|
573 | <t:tab id="spotdata" title="Spot data" |
---|
574 | visible="<%=hasDbSpots%>" /> |
---|
575 | |
---|
576 | <t:tab id="overviewplots" title="Overview plots" |
---|
577 | tooltip="Predefined plots for all bioassays in this bioassay set" |
---|
578 | visible="<%=overviewPlotInvoker.getNumExtensions() > 0%>"> |
---|
579 | <% |
---|
580 | if ("overviewplots".equals(tabId)) |
---|
581 | { |
---|
582 | ActionIterator<OverviewPlotAction> plots = overviewPlotInvoker.iterate(); |
---|
583 | StringBuilder script = new StringBuilder(); |
---|
584 | %> |
---|
585 | <t:tabcontrol id="overviewplots" switch="switchOverview"> |
---|
586 | <% |
---|
587 | while (plots.hasNext()) |
---|
588 | { |
---|
589 | OverviewPlotAction action = plots.next(); |
---|
590 | String baseId = plots.getExtension().getId() + "." + action.getId(); |
---|
591 | %> |
---|
592 | <t:tab |
---|
593 | tooltip="<%=action.getDescription() %>" |
---|
594 | title="<%=action.getTitle()%>" |
---|
595 | id="<%=baseId%>" |
---|
596 | > |
---|
597 | <% |
---|
598 | for (PlotGenerator generator : action.getPlotGenerators()) |
---|
599 | { |
---|
600 | String plotId = generator.getId(); |
---|
601 | script.append("registerImage('").append(baseId).append("','") |
---|
602 | .append(plotId).append("','") |
---|
603 | .append(HTML.javaScriptEncode(generator.getUrl())).append("');\n"); |
---|
604 | %><img id="<%=baseId + "." + plotId%>" |
---|
605 | class="plot" |
---|
606 | src="../../../images/transparent_pixel.gif" |
---|
607 | width="<%=generator.getWidth()%>" |
---|
608 | height="<%=generator.getHeight()%>" |
---|
609 | alt="<%=HTML.encodeTags(generator.getTitle())%>" |
---|
610 | >​​<% |
---|
611 | } |
---|
612 | %> |
---|
613 | </t:tab> |
---|
614 | <% |
---|
615 | } |
---|
616 | %> |
---|
617 | </t:tabcontrol> |
---|
618 | <script language="JavaScript"> |
---|
619 | <%=script%> |
---|
620 | </script> |
---|
621 | <% |
---|
622 | } |
---|
623 | %> |
---|
624 | </t:tab> |
---|
625 | </t:tabcontrol> |
---|
626 | |
---|
627 | </base:body> |
---|
628 | </base:page> |
---|
629 | <% |
---|
630 | } |
---|
631 | finally |
---|
632 | { |
---|
633 | if (dc != null) dc.close(); |
---|
634 | } |
---|
635 | |
---|
636 | %> |
---|