1 | <%@ page |
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2 | pageEncoding="UTF-8" |
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3 | session="false" |
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4 | import="net.sf.basedb.core.User" |
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5 | import="net.sf.basedb.core.DbControl" |
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6 | import="net.sf.basedb.core.SessionControl" |
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7 | import="net.sf.basedb.core.Application" |
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8 | import="net.sf.basedb.clients.web.Base" |
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9 | import="net.sf.basedb.clients.web.util.HTML" |
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10 | import="net.sf.basedb.clients.web.extensions.ExtensionsControl" |
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11 | %> |
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12 | <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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13 | <%@ taglib prefix="p" uri="/WEB-INF/path.tld" %> |
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14 | <% |
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15 | final SessionControl sc = Base.getExistingSessionControl(request, true); |
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16 | final String ID = sc.getId(); |
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17 | final float scale = Base.getScale(sc); |
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18 | final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie"); |
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19 | DbControl dc = null; |
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20 | try |
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21 | { |
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22 | dc = sc.newDbControl(); |
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23 | final User user = User.getById(dc, sc.getLoggedInUserId()); |
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24 | %> |
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25 | <base:page type="default" > |
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26 | <base:head scripts="ajax.js" styles="path.css"> |
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27 | <link rel="stylesheet" type="text/css" href="../css/reggie.css"> |
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28 | <script language="JavaScript" src="../reggie.js" type="text/javascript" charset="UTF-8"></script> |
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29 | |
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30 | <script language="JavaScript"> |
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31 | |
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32 | var debug = true; |
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33 | var currentStep = 1; |
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34 | |
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35 | var dateIsValid = []; |
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36 | var flowCellIsValid = []; |
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37 | var commentsIsValid = false; |
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38 | |
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39 | |
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40 | function init() |
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41 | { |
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42 | var frm = document.forms['reggie']; |
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43 | var flowCells = getFlowCells(); |
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44 | |
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45 | // Load existing Flow cells not yet registered |
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46 | if (flowCells != null && flowCells.length > 0) |
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47 | { |
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48 | for (var i=0; i < flowCells.length; i++) |
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49 | { |
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50 | var flowCell = flowCells[i]; |
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51 | var option = new Option(flowCell.name, flowCell.id, i < 2); |
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52 | option.flowCell = flowCell; |
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53 | frm.flowcells.options[frm.flowcells.length] = option; |
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54 | } |
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55 | setInputStatus('flowcells', '', 'valid'); |
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56 | outcomeOnChange(); |
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57 | } |
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58 | else |
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59 | { |
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60 | var msg = 'No flow cells available for processing.'; |
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61 | setFatalError(msg); |
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62 | return; |
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63 | } |
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64 | |
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65 | // All is ok |
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66 | frm.flowcells.focus(); |
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67 | } |
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68 | |
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69 | |
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70 | function goNextAuto() |
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71 | { |
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72 | goNext(false); |
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73 | } |
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74 | |
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75 | function goNext(manual) |
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76 | { |
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77 | setInnerHTML('gonext.message', ''); |
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78 | if (currentStep == 1) |
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79 | { |
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80 | gotoStep2(); |
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81 | } |
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82 | setCurrentStep(currentStep); |
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83 | } |
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84 | |
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85 | |
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86 | |
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87 | function getFlowCells() |
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88 | { |
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89 | var frm = document.forms['reggie']; |
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90 | |
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91 | var request = Ajax.getXmlHttpRequest(); |
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92 | try |
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93 | { |
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94 | showLoadingAnimation('Loading flow cells lists...'); |
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95 | var url = '../FlowCell.servlet?ID=<%=ID%>&cmd=GetUnprocessedFlowCells'; |
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96 | request.open("GET", url, false); |
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97 | request.send(null); |
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98 | } |
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99 | finally |
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100 | { |
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101 | hideLoadingAnimation(); |
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102 | } |
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103 | |
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104 | if (debug) Main.debug(request.responseText); |
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105 | var response = JSON.parse(request.responseText); |
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106 | if (response.status != 'ok') |
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107 | { |
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108 | setFatalError(response.message); |
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109 | return false; |
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110 | } |
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111 | return response.flowCells; |
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112 | } |
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113 | |
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114 | function gotoStep2() |
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115 | { |
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116 | var frm = document.forms['reggie']; |
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117 | |
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118 | var selectedFlowCells = []; |
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119 | for (var i = 0; i < frm.flowcells.length; i++) |
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120 | { |
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121 | if (frm.flowcells[i].selected) |
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122 | { |
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123 | selectedFlowCells[selectedFlowCells.length] = frm.flowcells[i].flowCell; |
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124 | } |
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125 | } |
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126 | |
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127 | if (selectedFlowCells.length == 0) |
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128 | { |
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129 | setInputStatus('flowcells', 'Select at least 1 flow cell', 'invalid'); |
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130 | return; |
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131 | } |
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132 | |
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133 | |
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134 | frm.flowcells.disabled = true; |
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135 | frm.outcome[0].disabled = true; |
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136 | frm.outcome[1].disabled = true; |
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137 | |
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138 | currentStep = 2; |
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139 | Main.show('step.2.section'); |
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140 | Main.addClass(document.getElementById('step.1.section'), 'disabled'); |
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141 | Main.hide('gonext'); |
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142 | Main.show('gocancel'); |
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143 | Main.show('goregister'); |
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144 | |
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145 | var html = '<tr valign="top">'; |
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146 | html += '<td class="prompt">Flow cell</td>'; |
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147 | html += '<td style="width: 11em;"><b>ID</b></td>'; |
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148 | html += '<td><b>ReadString</b></td>'; |
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149 | html += '<td class="status"></td>'; |
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150 | html += '<td class="help" rowspan="' + (selectedFlowCells.length+1) +'">'; |
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151 | html += 'ID and ReadString is required for registration. '; |
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152 | html += 'ReadString must be a sequence of letters <b>Y</b>, <b>N</b>, <b>I</b>, <b>J</b> followed by digits.'; |
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153 | html += '</td>'; |
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154 | html += '</tr>'; |
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155 | |
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156 | for (var i = 0; i < selectedFlowCells.length; i++) |
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157 | { |
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158 | var fc = selectedFlowCells[i]; |
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159 | var prefix = 'fc.'+fc.id; |
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160 | html += '<tr>'; |
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161 | html += '<td class="subprompt">'+fc.name+'</td>'; |
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162 | html += '<td><input type="text" class="required" name="'+prefix+'.id" onblur="flowCellIdOnBlur('+fc.id+')"></td>'; |
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163 | html += '<td><input type="text" class="required" name="'+prefix+'.readString" onblur="readStringOnBlur('+fc.id+')" value="'+fc.ReadString+'"></td>'; |
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164 | html += '<td class="status" id="'+prefix+'.status">'; |
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165 | html += '</tr>'; |
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166 | } |
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167 | |
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168 | setInnerHTML('fc-data', html); |
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169 | |
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170 | // Load mRNA protocols |
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171 | var clusterProtocols = getProtocols('CLUSTER_PROTOCOL'); |
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172 | for (var i = 0; i < clusterProtocols.length; i++) |
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173 | { |
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174 | var protocol = clusterProtocols[i]; |
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175 | frm.clusterProtocol[frm.clusterProtocol.length] = new Option(protocol.name, protocol.id, protocol.isDefault); |
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176 | setInputStatus('clusterProtocol', '', 'valid'); |
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177 | } |
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178 | if (frm.clusterProtocol.length == 0) |
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179 | { |
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180 | frm.clusterProtocol[0] = new Option('- none -', ''); |
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181 | } |
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182 | |
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183 | frm['fc.'+selectedFlowCells[0].id+'.id'].focus(); |
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184 | } |
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185 | |
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186 | function getProtocols(subtype) |
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187 | { |
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188 | var request = Ajax.getXmlHttpRequest(); |
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189 | try |
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190 | { |
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191 | showLoadingAnimation('Loading ' + subtype + ' protocols...'); |
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192 | var url = '../Protocol.servlet?ID=<%=ID%>&cmd=GetProtocols&subtype='+subtype; |
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193 | request.open("GET", url, false); |
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194 | request.send(null); |
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195 | } |
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196 | finally |
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197 | { |
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198 | hideLoadingAnimation(); |
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199 | } |
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200 | |
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201 | if (debug) Main.debug(request.responseText); |
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202 | var response = JSON.parse(request.responseText); |
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203 | if (response.status != 'ok') |
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204 | { |
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205 | setFatalError(response.message); |
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206 | return false; |
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207 | } |
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208 | return response.protocols; |
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209 | } |
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210 | |
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211 | function outcomeOnChange() |
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212 | { |
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213 | var frm = document.forms['reggie']; |
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214 | Main.addOrRemoveClass(frm['comments'], 'required', document.getElementById('outcomeFailed').checked); |
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215 | commentsOnChange(); |
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216 | } |
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217 | |
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218 | function dateOnChange(dateField) |
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219 | { |
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220 | var frm = document.forms['reggie']; |
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221 | |
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222 | setInputStatus(dateField, '', ''); |
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223 | dateIsValid[dateField] = true; |
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224 | var date = frm[dateField].value; |
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225 | |
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226 | if (date == '') |
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227 | { |
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228 | setInputStatus(dateField, 'Missing date', 'warning'); |
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229 | return; |
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230 | } |
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231 | |
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232 | // Auto-fill the date if it's only given with 4(MMdd) or 6(yyMMdd) digits. |
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233 | date = autoFillDate(date); |
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234 | frm[dateField].value = date; |
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235 | if (!Dates.isDate(date, 'yyyyMMdd')) |
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236 | { |
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237 | setInputStatus(dateField, 'Not a valid date', 'invalid'); |
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238 | dateIsValid[dateField] = false; |
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239 | return; |
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240 | } |
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241 | |
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242 | setInputStatus(dateField, '', 'valid'); |
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243 | } |
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244 | |
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245 | function setDate(frmName, dateField, date) |
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246 | { |
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247 | var frm = document.forms['reggie']; |
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248 | frm[dateField].value = date; |
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249 | dateOnChange(dateField); |
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250 | frm[dateField].focus(); |
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251 | } |
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252 | |
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253 | function commentsOnChange() |
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254 | { |
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255 | var frm = document.forms['reggie']; |
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256 | commentsIsValid = false; |
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257 | setInputStatus('comments', '', ''); |
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258 | |
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259 | var comments = frm.comments.value; |
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260 | |
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261 | if (comments == '' && document.getElementById('outcomeFailed').checked) |
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262 | { |
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263 | setInputStatus('comments', 'Missing', 'invalid'); |
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264 | return; |
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265 | } |
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266 | |
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267 | setInputStatus('comments', '', 'valid'); |
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268 | commentsIsValid = true; |
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269 | } |
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270 | |
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271 | function flowCellIdOnBlur(flowCellId) |
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272 | { |
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273 | checkFlowCellData(flowCellId); |
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274 | } |
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275 | |
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276 | function readStringOnBlur(flowCellId) |
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277 | { |
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278 | checkFlowCellData(flowCellId); |
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279 | } |
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280 | |
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281 | function checkFlowCellData(flowCellId) |
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282 | { |
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283 | var frm = document.forms['reggie']; |
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284 | |
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285 | var prefix = 'fc.'+flowCellId; |
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286 | setInputStatus(prefix, '', ''); |
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287 | |
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288 | flowCellIsValid[prefix+'.id'] = false; |
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289 | flowCellIsValid[prefix+'.readString'] = false; |
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290 | |
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291 | var id = frm[prefix+'.id'].value; |
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292 | if (id == '') |
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293 | { |
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294 | setInputStatus(prefix, 'ID is a required value', 'invalid'); |
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295 | return; |
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296 | } |
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297 | |
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298 | flowCellIsValid[prefix+'.id'] = true; |
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299 | |
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300 | var readString = frm[prefix+'.readString'].value; |
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301 | if (readString == '') |
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302 | { |
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303 | setInputStatus(prefix, 'ReadString is a required value', 'invalid'); |
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304 | return; |
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305 | } |
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306 | |
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307 | if (!readString.match(/^([YNIJ]\d+)+$/)) |
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308 | { |
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309 | setInputStatus(prefix, 'Not a valid ReadString value', 'invalid'); |
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310 | return; |
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311 | } |
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312 | |
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313 | flowCellIsValid[prefix+'.readString'] = true; |
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314 | setInputStatus(prefix, '', 'valid'); |
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315 | } |
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316 | |
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317 | function step2IsValid() |
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318 | { |
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319 | if (!commentsIsValid) return false; |
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320 | |
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321 | if (dateIsValid['clusterDate'] == false) return false; |
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322 | if (dateIsValid['sequenceStartDate'] == false) return false; |
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323 | |
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324 | var frm = document.forms['reggie']; |
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325 | for (var i = 0; i < frm.flowcells.length; i++) |
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326 | { |
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327 | if (frm.flowcells[i].selected) |
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328 | { |
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329 | var fc = frm.flowcells[i].flowCell; |
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330 | Main.debug(fc.name + ':'+ fc.id + ':' + flowCellIsValid['fc.'+fc.id+'.id'] + ':' + flowCellIsValid['fc.'+fc.id+'.readString']); |
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331 | if (flowCellIsValid['fc.'+fc.id+'.id'] != true) return false; |
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332 | if (flowCellIsValid['fc.'+fc.id+'.readString'] != true) return false; |
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333 | } |
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334 | } |
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335 | |
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336 | return true; |
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337 | } |
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338 | |
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339 | function goRegister() |
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340 | { |
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341 | if (!step2IsValid()) return; |
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342 | var frm = document.forms['reggie']; |
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343 | |
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344 | Main.hide('goregister'); |
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345 | Main.hide('gocancel'); |
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346 | Main.addClass(document.getElementById('step.2.section'), 'disabled'); |
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347 | |
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348 | frm.clusterDate.disabled = true; |
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349 | frm.clusterOperator.disabled = true; |
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350 | frm.sequenceStartDate.disabled = true; |
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351 | frm.sequenceOperator.disabled = true; |
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352 | frm.clusterProtocol.disabled = true; |
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353 | frm.comments.disabled = true; |
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354 | |
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355 | var submitInfo = {}; |
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356 | submitInfo.flowCells = []; |
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357 | for (var i = 0; i < frm.flowcells.length; i++) |
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358 | { |
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359 | if (frm.flowcells[i].selected) |
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360 | { |
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361 | var fc = frm.flowcells[i].flowCell; |
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362 | fc.externalId = frm['fc.'+fc.id+'.id'].value; |
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363 | fc.ReadString = frm['fc.'+fc.id+'.readString'].value; |
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364 | submitInfo.flowCells[submitInfo.flowCells.length] = fc; |
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365 | } |
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366 | } |
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367 | |
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368 | submitInfo.clusterProtocol = parseInt(frm.clusterProtocol.value, 10); |
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369 | submitInfo.failed = document.getElementById('outcomeSuccess').checked ? false : true; |
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370 | submitInfo.clusterDate = frm.clusterDate.value; |
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371 | submitInfo.clusterOperator = frm.clusterOperator.value; |
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372 | submitInfo.sequenceStartDate = frm.sequenceStartDate.value; |
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373 | submitInfo.sequenceOperator = frm.sequenceOperator.value; |
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374 | submitInfo.comments = frm.comments.value; |
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375 | |
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376 | if (debug) Main.debug(JSON.stringify(submitInfo)); |
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377 | var url = '../FlowCell.servlet?ID=<%=ID%>&cmd=RegisterFlowCells'; |
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378 | |
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379 | var request = Ajax.getXmlHttpRequest(); |
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380 | try |
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381 | { |
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382 | showLoadingAnimation('Performing registration...'); |
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383 | request.open("POST", url, false); |
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384 | request.send(JSON.stringify(submitInfo)); |
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385 | } |
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386 | finally |
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387 | { |
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388 | hideLoadingAnimation(); |
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389 | } |
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390 | |
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391 | if (debug) Main.debug(request.responseText); |
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392 | var response = JSON.parse(request.responseText); |
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393 | |
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394 | if (response.messages && response.messages.length > 0) |
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395 | { |
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396 | var msg = '<ul>'; |
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397 | for (var i = 0; i < response.messages.length; i++) |
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398 | { |
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399 | var msgLine = response.messages[i]; |
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400 | if (msgLine.indexOf('[Warning]') >= 0) |
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401 | { |
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402 | msg += '<li class="warning">' + msgLine.replace('[Warning]', ''); |
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403 | } |
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404 | else |
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405 | { |
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406 | msg += '<li>' + msgLine; |
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407 | } |
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408 | } |
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409 | msg += '</ul>'; |
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410 | setInnerHTML('messages', msg); |
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411 | Main.show('messages'); |
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412 | } |
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413 | |
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414 | if (response.status != 'ok') |
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415 | { |
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416 | Main.addClass(document.getElementById('messages'), 'failure'); |
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417 | setFatalError(response.message); |
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418 | return false; |
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419 | } |
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420 | |
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421 | Main.show('gorestart'); |
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422 | } |
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423 | |
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424 | |
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425 | </script> |
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426 | |
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427 | </base:head> |
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428 | <base:body onload="init()"> |
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429 | |
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430 | <p:path><p:pathelement |
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431 | title="Reggie" href="<%="../index.jsp?ID="+ID%>" |
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432 | /><p:pathelement title="Flow cell registration" |
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433 | /></p:path> |
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434 | |
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435 | <div class="content"> |
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436 | <% |
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437 | if (sc.getActiveProjectId() == 0) |
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438 | { |
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439 | %> |
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440 | <div class="messagecontainer note" style="width: 950px; margin-left: 20px; margin-bottom: 20px; margin-right: 0px; font-weight: bold; color: #cc0000;"> |
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441 | No project has been selected. You may proceed with the registration but |
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442 | created items will not be shared. |
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443 | </div> |
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444 | <% |
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445 | } |
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446 | %> |
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447 | |
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448 | <form name="reggie" onsubmit="return false;"> |
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449 | <input type="hidden" name="pdf.id" value=""> |
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450 | |
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451 | <div id="step.1.section"> |
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452 | <table class="stepform"> |
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453 | <tr> |
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454 | <td rowspan="3" class="stepno">1</td> |
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455 | <td class="steptitle">Select flow cells</td> |
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456 | </tr> |
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457 | <tr> |
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458 | <td class="stepfields"> |
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459 | <table> |
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460 | <tr valign="top"> |
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461 | <td class="prompt">Flow cells</td> |
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462 | <td class="input"><select class="required" style="width:90%;" |
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463 | name="flowcells" id="flowcells" multiple size="4"></select> |
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464 | </td> |
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465 | <td class="status" id="flowcells.status"></td> |
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466 | <td class="help"><span id="flowcells.message" class="message" style="display: none;"></span> |
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467 | Select one or more existing flow cells. The list contain all flow cells that |
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468 | has not yet been processed (determined by the absence of a 'creation' date). |
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469 | </td> |
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470 | </tr> |
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471 | <tr valign="top"> |
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472 | <td class="prompt">Outcome</td> |
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473 | <td class="input"> |
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474 | <input type="radio" name="outcome" id="outcomeSuccess" |
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475 | onchange="outcomeOnChange()" checked><label for="outcomeSuccess">Success</label> - continue with sequencing<br> |
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476 | <input type="radio" name="outcome" id="outcomeFailed" |
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477 | onchange="outcomeOnChange()"><label for="outcomeFailed">Failure</label> - no sequencing |
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478 | </td> |
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479 | <td class="status"></td> |
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480 | <td class="help"> |
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481 | Select the <b>Failure</b> option if it is not possible to continue |
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482 | with sequencing. RNA will be flagged and added |
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483 | to the <b>Flagged RNA</b> list. |
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484 | </td> |
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485 | </tr> |
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486 | </table> |
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487 | </td> |
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488 | </tr> |
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489 | </table> |
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490 | </div> |
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491 | |
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492 | <div id="step.2.section" style="display: none;"> |
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493 | <table class="stepform"> |
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494 | <tr> |
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495 | <td rowspan="3" class="stepno">2</td> |
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496 | <td class="steptitle">Clustering information</td> |
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497 | </tr> |
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498 | <tr> |
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499 | <td class="stepfields"> |
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500 | <table> |
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501 | <tbody id="fc-data"></tbody> |
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502 | <tr valign="top"> |
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503 | <td class="prompt">Step</td> |
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504 | <td style="width: 11em;"><b>Date</b></td> |
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505 | <td><b>Operator</b></td> |
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506 | <td class="status"></td> |
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507 | <td class="help" rowspan="3"> |
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508 | Enter date and operator for each step in the clustering and sequencing startup. |
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509 | (YYYYMMDD or MMDD) |
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510 | </td> |
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511 | </tr> |
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512 | <tr> |
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513 | <td class="subprompt">Clustering</td> |
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514 | <td> |
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515 | <input type="text" name="clusterDate" maxlength="10" style="width: 8em;" |
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516 | onblur="dateOnChange('clusterDate')" onkeypress="focusOnEnter(event, 'clusterOperator')"> |
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517 | <base:icon |
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518 | onclick="Dates.selectDate('Cluster date', 'reggie', 'clusterDate', 'setDate', 'yyyyMMdd')" |
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519 | image="calendar.png" |
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520 | tooltip="Select a date from a calendar" |
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521 | tabindex="-1" |
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522 | /> |
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523 | </td> |
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524 | <td> |
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525 | <input type="text" name="clusterOperator" value="<%=HTML.encodeTags(user.getName()) %>" |
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526 | style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'sequenceStartDate')"> |
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527 | </td> |
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528 | <td class="status" id="clusterDate.status"></td> |
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529 | </tr> |
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530 | <tr> |
---|
531 | <td class="subprompt">Sequence start</td> |
---|
532 | <td> |
---|
533 | <input type="text" name="sequenceStartDate" maxlength="10" style="width: 8em;" |
---|
534 | onblur="dateOnChange('sequenceStartDate')" onkeypress="focusOnEnter(event, 'sequenceOperator')"> |
---|
535 | <base:icon |
---|
536 | onclick="Dates.selectDate('Sequence start date', 'reggie', 'sequenceStartDate', 'setDate', 'yyyyMMdd')" |
---|
537 | image="calendar.png" |
---|
538 | tooltip="Select a date from a calendar" |
---|
539 | tabindex="-1" |
---|
540 | /> |
---|
541 | </td> |
---|
542 | <td> |
---|
543 | <input type="text" name="sequenceOperator" value="<%=HTML.encodeTags(user.getName()) %>" |
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544 | style="width: 95%;" maxlength="255" onkeypress="focusOnEnter(event, 'clusterProtocol')"> |
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545 | </td> |
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546 | <td class="status" id="sequenceStartDate.status"></td> |
---|
547 | </tr> |
---|
548 | <tr valign="top"> |
---|
549 | <td class="prompt">Protocol</td> |
---|
550 | <td class="input" colspan="2"><select style="width:90%" name="clusterProtocol" id="clusterProtocol" |
---|
551 | onkeypress="focusOnEnter(event, 'comments')"></select></td> |
---|
552 | <td class="status" id="clusterProtocol.status"></td> |
---|
553 | <td class="help"><span id="clusterProtocol.message" class="message" style="display: none;"></span> |
---|
554 | Select the protocol which was used in the clustering. |
---|
555 | </td> |
---|
556 | </tr> |
---|
557 | <tr valign="top"> |
---|
558 | <td class="prompt">Comments</td> |
---|
559 | <td class="input" colspan="2"><textarea rows="4" cols="50" style="width: 90%;" name="comments" value="" onblur="commentsOnChange()"></textarea></td> |
---|
560 | <td class="status" id="comments.status"></td> |
---|
561 | <td class="help"><span id="comments.message" class="message" style="display: none;"></span>Comments about the clustering.</td> |
---|
562 | </tr> |
---|
563 | </table> |
---|
564 | </td> |
---|
565 | </tr> |
---|
566 | </table> |
---|
567 | </div> |
---|
568 | |
---|
569 | <div class="loading" id="loading" style="display: none;"><table><tr><td><img src="../images/loading.gif"></td><td id="loading.msg">Please wait...</td></tr></table></div> |
---|
570 | |
---|
571 | <div class="messagecontainer error" id="errorMessage" style="display: none; width: 950px; margin-left: 20px; margin-bottom: 0px;"></div> |
---|
572 | |
---|
573 | <div id="messages" class="success" style="display: none; width: 950px; margin-left: 20px; margin-top: 20px;"></div> |
---|
574 | |
---|
575 | <table style="margin-left: 20px; margin-top: 10px;" class="navigation"> |
---|
576 | <tr> |
---|
577 | <td><base:button id="gocancel" title="Cancel" onclick="goRestart(false)" style="display: none;"/></td> |
---|
578 | <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" onclick="goNext(true)"/></td> |
---|
579 | <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>" onclick="goRegister()" style="display: none;"/></td> |
---|
580 | <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" onclick="goRestart(true)" style="display: none;"/></td> |
---|
581 | <td id="gonext.message" class="message"></td> |
---|
582 | </tr> |
---|
583 | </table> |
---|
584 | |
---|
585 | </form> |
---|
586 | </div> |
---|
587 | |
---|
588 | </base:body> |
---|
589 | </base:page> |
---|
590 | <% |
---|
591 | } |
---|
592 | finally |
---|
593 | { |
---|
594 | if (dc != null) dc.close(); |
---|
595 | } |
---|
596 | %> |
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