1 | <?xml version="1.0" encoding="UTF-8" ?> |
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2 | <extensions xmlns="http://base.thep.lu.se/extensions.xsd"> |
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3 | <about safe-resources="1"> |
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4 | <name>Reggie package</name> |
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5 | <description> |
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6 | A package for simplified registration of biosources |
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7 | and samples. |
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8 | </description> |
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9 | <version>4.44-dev</version> |
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10 | <min-base-version>3.19.0</min-base-version> |
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11 | <copyright>BASE development team</copyright> |
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12 | <email>basedb-users@lists.sourceforge.net</email> |
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13 | <url>https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie</url> |
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14 | </about> |
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15 | |
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16 | <plugin-definition id="CaliperSampleNameExporter"> |
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17 | <about> |
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18 | <name>Caliper sample name exporter</name> |
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19 | <description> |
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20 | Plug-in that export the sample names on a bioplate to a |
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21 | CSV file that can be used by the Caliper software. The |
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22 | exported file has one line for each non-empty well with |
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23 | five columns. Only the first two columns are used: |
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24 | Well coordinate, sample name. |
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25 | </description> |
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26 | </about> |
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27 | <plugin-class>net.sf.basedb.reggie.plugins.CaliperSampleNameExporter</plugin-class> |
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28 | <settings> |
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29 | <property name="everyone-use">1</property> |
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30 | <property name="immediate-execution">1</property> |
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31 | </settings> |
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32 | </plugin-definition> |
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33 | |
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34 | <plugin-definition id="CaliperRunParametersExporter"> |
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35 | <about> |
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36 | <name>Caliper run parameters exporter</name> |
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37 | <description> |
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38 | Plug-in that export run file parameters that can be used by the |
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39 | Caliper software. The run file include information about Assay Type, |
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40 | Plate Name, selected wells, etc. |
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41 | </description> |
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42 | </about> |
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43 | <plugin-class>net.sf.basedb.reggie.plugins.CaliperRunParametersExporter</plugin-class> |
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44 | <settings> |
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45 | <property name="everyone-use">1</property> |
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46 | <property name="immediate-execution">1</property> |
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47 | </settings> |
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48 | </plugin-definition> |
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49 | |
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50 | <plugin-definition id="CaliperLibPrepParametersExporter"> |
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51 | <about> |
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52 | <name>Caliper library preparation parameters exporter</name> |
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53 | <description> |
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54 | Plug-in that export run file parameters that can be used by the |
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55 | Caliper software. The run file include information about Assay Type, |
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56 | Plate Name, selected wells, etc. |
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57 | </description> |
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58 | </about> |
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59 | <plugin-class>net.sf.basedb.reggie.plugins.CaliperLibPrepParametersExporter</plugin-class> |
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60 | <settings> |
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61 | <property name="everyone-use">1</property> |
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62 | <property name="immediate-execution">1</property> |
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63 | </settings> |
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64 | </plugin-definition> |
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65 | |
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66 | <plugin-definition id="QubitSampleNameExporter"> |
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67 | <about> |
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68 | <name>Qubit sample name exporter</name> |
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69 | <description> |
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70 | Plug-in that export the sample names on a bioplate to a |
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71 | tab-separated file that the operator can use to fill in |
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72 | concentration measurements from the Qubit. When all data |
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73 | has been filled in, the file can be uploaded to BASE and |
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74 | the concentration values are imported as annotations. |
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75 | </description> |
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76 | </about> |
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77 | <plugin-class>net.sf.basedb.reggie.plugins.QubitSampleNameExporter</plugin-class> |
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78 | <settings> |
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79 | <property name="everyone-use">1</property> |
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80 | <property name="immediate-execution">1</property> |
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81 | </settings> |
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82 | </plugin-definition> |
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83 | <plugin-definition id="MBafPlotterPlugin"> |
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84 | <about> |
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85 | <name>mBAF plotter plug-in</name> |
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86 | <description> |
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87 | Plug-in for extracting and plotting mBAF data from existing |
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88 | VCF files. |
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89 | </description> |
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90 | </about> |
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91 | <plugin-class>net.sf.basedb.reggie.plugins.MBafPlotterPlugin</plugin-class> |
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92 | <settings> |
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93 | <property name="everyone-use">0</property> |
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94 | <property name="immediate-execution">1</property> |
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95 | </settings> |
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96 | </plugin-definition> |
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97 | |
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98 | <plugin-definition id="GeneReportPlugin"> |
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99 | <about> |
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100 | <name>Report creator</name> |
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101 | <description> |
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102 | Plug-in for generating reports of cufflinks data. |
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103 | </description> |
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104 | </about> |
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105 | <plugin-class>net.sf.basedb.reggie.plugins.GeneReportPlugin</plugin-class> |
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106 | <settings> |
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107 | <property name="everyone-use">0</property> |
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108 | <property name="immediate-execution">1</property> |
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109 | </settings> |
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110 | </plugin-definition> |
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111 | <plugin-definition id="ReportsCombinerPlugin"> |
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112 | <about> |
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113 | <name>Report combiner</name> |
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114 | <description> |
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115 | Plug-in for combining multiple existing |
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116 | reports to a single PDF/ZIP file and adding |
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117 | personal information about the patients. |
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118 | </description> |
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119 | </about> |
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120 | <plugin-class>net.sf.basedb.reggie.plugins.GeneReportsCombinerPlugin</plugin-class> |
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121 | <settings> |
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122 | <property name="everyone-use">0</property> |
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123 | <property name="immediate-execution">1</property> |
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124 | </settings> |
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125 | </plugin-definition> |
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126 | <plugin-definition id="ReleaseExporterPlugin"> |
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127 | <about> |
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128 | <name>Release exporter</name> |
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129 | <description> |
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130 | Plug-in for exporting released data based |
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131 | on raw bioassays in a list. |
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132 | </description> |
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133 | </about> |
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134 | <plugin-class>net.sf.basedb.reggie.plugins.release.ReleaseExporterPlugin</plugin-class> |
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135 | <settings> |
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136 | <property name="everyone-use">0</property> |
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137 | </settings> |
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138 | </plugin-definition> |
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139 | <plugin-definition id="TMASpecimenImporter"> |
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140 | <about> |
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141 | <name>TMA Specimen importer</name> |
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142 | <description> |
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143 | Plug-in for importing TMA specimen. |
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144 | </description> |
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145 | </about> |
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146 | <plugin-class>net.sf.basedb.reggie.plugins.TMASpecimenImporter</plugin-class> |
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147 | <settings> |
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148 | <property name="everyone-use">0</property> |
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149 | </settings> |
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150 | </plugin-definition> |
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151 | <plugin-definition id="SingleSamplePredictorPlugin"> |
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152 | <about> |
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153 | <name>Single Sample Predictor plug-in</name> |
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154 | <description> |
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155 | Plug-in for running Single Sample Predictor models on raw |
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156 | bioassays with StringTie data. |
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157 | </description> |
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158 | </about> |
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159 | <plugin-class>net.sf.basedb.reggie.ssp.SspPlugin</plugin-class> |
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160 | <settings> |
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161 | <property name="everyone-use">0</property> |
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162 | </settings> |
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163 | </plugin-definition> |
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164 | <plugin-definition id="SetPermissionsForDelivery"> |
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165 | <about> |
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166 | <name>Set access permissions for delivery</name> |
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167 | <description> |
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168 | Plug-in for setting access permissions on items that |
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169 | are delivered to sites. This plug-in can't be used |
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170 | interactively. The plug-in gains elevated permissions |
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171 | for setting permissions on items that the user would |
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172 | normally not be allowed to change. |
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173 | </description> |
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174 | </about> |
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175 | <plugin-class>net.sf.basedb.reggie.plugins.SetPermissionsForDeliveryPlugin</plugin-class> |
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176 | <settings> |
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177 | <property name="everyone-use">0</property> |
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178 | </settings> |
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179 | </plugin-definition> |
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180 | <extension |
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181 | id="net.sf.basedb.reggie" |
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182 | extends="net.sf.basedb.clients.web.menu.extensions" |
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183 | > |
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184 | <index>10</index> |
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185 | <about safe-scripts="1"> |
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186 | <name>Reggie</name> |
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187 | <description> |
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188 | Menu entry for accessing reggie-specific operations. |
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189 | </description> |
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190 | </about> |
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191 | <action-factory> |
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192 | <factory-class> |
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193 | net.sf.basedb.reggie.extensions.MenuItemFactory |
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194 | </factory-class> |
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195 | <parameters> |
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196 | <title>Reggie</title> |
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197 | <icon>~/images/snake-icon.png</icon> |
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198 | <tooltip>Access reggie operations</tooltip> |
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199 | <data-url>~/index.jsp?ID=$SESSION-ID$</data-url> |
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200 | </parameters> |
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201 | </action-factory> |
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202 | </extension> |
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203 | |
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204 | <extension |
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205 | id="net.sf.basedb.reggie.start-page" |
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206 | extends="net.sf.basedb.clients.web.start-page" |
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207 | > |
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208 | <index>10</index> |
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209 | <about> |
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210 | <name>Reggie</name> |
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211 | <description> |
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212 | Use the Reggie index page as a start page. |
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213 | </description> |
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214 | </about> |
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215 | <action-factory> |
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216 | <factory-class> |
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217 | net.sf.basedb.reggie.extensions.StartPageFactory |
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218 | </factory-class> |
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219 | <parameters> |
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220 | <name>Extensions › Reggie</name> |
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221 | <url>~/index.jsp?ID=$SESSION-ID$</url> |
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222 | <description>Use Reggie as the start page</description> |
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223 | </parameters> |
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224 | </action-factory> |
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225 | </extension> |
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226 | |
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227 | |
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228 | <extension |
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229 | id="net.sf.basedb.reggie.toolbar.case-summary" |
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230 | > |
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231 | <extends> |
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232 | <ref index="1">net.sf.basedb.clients.web.toolbar.item.sample</ref> |
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233 | <ref index="1">net.sf.basedb.clients.web.toolbar.item.extract</ref> |
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234 | <ref index="1">net.sf.basedb.clients.web.toolbar.item.derivedbioassay</ref> |
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235 | <ref index="1">net.sf.basedb.clients.web.toolbar.item.rawbioassay</ref> |
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236 | </extends> |
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237 | <about safe-scripts="1"> |
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238 | <name>Case summary</name> |
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239 | <description> |
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240 | Adds a button to the toolbar of sample, extracts, derived and |
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241 | raw bioassay pages that opens the 'case summary' for the case that the current |
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242 | item is part of. Works for all items that have a name pattern |
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243 | that starts with 7 digits. |
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244 | </description> |
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245 | </about> |
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246 | <action-factory> |
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247 | <factory-class> |
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248 | net.sf.basedb.reggie.extensions.CaseSummaryButtonFactory |
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249 | </factory-class> |
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250 | <parameters> |
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251 | <title>Case summary</title> |
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252 | <clazz>button auto-init</clazz> |
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253 | <data-auto-init>reggie-case-summary-link</data-auto-init> |
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254 | <data-home>$HOME$</data-home> |
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255 | <icon>~/images/case_summary.png</icon> |
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256 | <script>~/scripts/case-summary.js</script> |
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257 | <stylesheet>~/css/reggie-inside-base.css</stylesheet> |
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258 | </parameters> |
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259 | </action-factory> |
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260 | </extension> |
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261 | |
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262 | <extension |
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263 | id="net.sf.basedb.reggie.list-column" |
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264 | > |
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265 | <extends> |
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266 | <ref index="1">net.sf.basedb.clients.web.listcolumn.sample</ref> |
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267 | <ref index="1">net.sf.basedb.clients.web.listcolumn.extract</ref> |
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268 | <ref index="1">net.sf.basedb.clients.web.listcolumn.derivedbioassay</ref> |
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269 | <ref index="1">net.sf.basedb.clients.web.listcolumn.rawbioassay</ref> |
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270 | <ref index="1">net.sf.basedb.clients.web.listcolumn.bioplate</ref> |
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271 | <ref index="1">net.sf.basedb.clients.web.listcolumn.job</ref> |
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272 | </extends> |
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273 | <index>2</index> |
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274 | <about safe-scripts="1"> |
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275 | <name>Reggie column</name> |
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276 | <description> |
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277 | Add a column to the list page of samples, extract, derived bioassays, |
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278 | raw bioassays and bioplates for including some reggie-specific links. |
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279 | </description> |
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280 | </about> |
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281 | <action-factory> |
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282 | <factory-class> |
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283 | net.sf.basedb.reggie.extensions.ReggieListColumnsFactory |
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284 | </factory-class> |
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285 | </action-factory> |
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286 | </extension> |
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287 | |
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288 | <extension |
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289 | id="net.sf.basedb.reggie.histology-thumbnail-column" |
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290 | extends="net.sf.basedb.clients.web.listcolumn.sample" |
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291 | > |
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292 | <index>3</index> |
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293 | <about safe-scripts="1"> |
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294 | <name>Stained image</name> |
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295 | <description> |
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296 | Add a column to the list page of samples that display |
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297 | a thumbnail of the stained histology image. |
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298 | </description> |
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299 | </about> |
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300 | <action-factory> |
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301 | <factory-class> |
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302 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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303 | </factory-class> |
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304 | <parameters> |
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305 | <id>his-image</id> |
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306 | <title>Stained image</title> |
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307 | <link-name>image</link-name> |
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308 | <subtype>STAINED</subtype> |
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309 | </parameters> |
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310 | </action-factory> |
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311 | </extension> |
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312 | |
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313 | <extension |
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314 | id="net.sf.basedb.reggie.ndpi-thumbnail-column" |
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315 | extends="net.sf.basedb.clients.web.listcolumn.bioplate" |
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316 | > |
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317 | <index>3</index> |
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318 | <about safe-scripts="1"> |
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319 | <name>NDPI image</name> |
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320 | <description> |
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321 | Add a column to the list page of bioplates that display |
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322 | a thumbnail of the NDPI image for HE glass slides. |
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323 | </description> |
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324 | </about> |
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325 | <action-factory> |
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326 | <factory-class> |
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327 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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328 | </factory-class> |
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329 | <parameters> |
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330 | <id>ndpi-thumbnail</id> |
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331 | <title>NDPI thumbnail</title> |
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332 | <link-name>NDPI Image</link-name> |
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333 | <platetype>HE_GLASS</platetype> |
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334 | </parameters> |
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335 | </action-factory> |
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336 | </extension> |
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337 | |
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338 | <extension |
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339 | id="net.sf.basedb.reggie.genereport-thumbnail-column" |
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340 | extends="net.sf.basedb.clients.web.listcolumn.rawbioassay" |
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341 | > |
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342 | <index>3</index> |
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343 | <about safe-scripts="1"> |
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344 | <name>Gene report PDF</name> |
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345 | <description> |
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346 | Add a column to the list page of raw bioassays that display |
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347 | a thumbnail of the gene report PDF. |
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348 | </description> |
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349 | </about> |
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350 | <action-factory> |
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351 | <factory-class> |
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352 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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353 | </factory-class> |
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354 | <parameters> |
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355 | <id>genereport-pdf</id> |
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356 | <title>Gene report</title> |
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357 | <link-name>genereport.pdf</link-name> |
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358 | <rawdatatype>CUFFLINKS</rawdatatype> |
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359 | </parameters> |
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360 | </action-factory> |
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361 | </extension> |
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362 | |
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363 | <extension |
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364 | id="net.sf.basedb.reggie.pilot-thumbnail-column" |
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365 | extends="net.sf.basedb.clients.web.listcolumn.rawbioassay" |
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366 | > |
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367 | <index>4</index> |
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368 | <about safe-scripts="1"> |
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369 | <name>Pilot report PDF</name> |
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370 | <description> |
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371 | Add a column to the list page of raw bioassays that display |
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372 | a thumbnail of the pilot report PDF. |
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373 | </description> |
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374 | </about> |
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375 | <action-factory> |
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376 | <factory-class> |
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377 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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378 | </factory-class> |
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379 | <parameters> |
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380 | <id>pilotreport-pdf</id> |
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381 | <title>Pilot report</title> |
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382 | <link-name>pilotreport.pdf</link-name> |
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383 | <rawdatatype>CUFFLINKS</rawdatatype> |
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384 | </parameters> |
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385 | </action-factory> |
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386 | </extension> |
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387 | |
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388 | <extension |
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389 | id="net.sf.basedb.reggie.scanbreport-thumbnail-column" |
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390 | extends="net.sf.basedb.clients.web.listcolumn.rawbioassay" |
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391 | > |
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392 | <index>3</index> |
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393 | <about safe-scripts="1"> |
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394 | <name>SCAN-B report PDF</name> |
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395 | <description> |
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396 | Add a column to the list page of raw bioassays that display |
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397 | a thumbnail of the SCAN-B report PDF. |
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398 | </description> |
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399 | </about> |
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400 | <action-factory> |
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401 | <factory-class> |
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402 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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403 | </factory-class> |
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404 | <parameters> |
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405 | <id>scanbreport-pdf</id> |
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406 | <title>SCAN-B report</title> |
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407 | <link-name>scanbreport.pdf</link-name> |
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408 | <rawdatatype>STRINGTIE</rawdatatype> |
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409 | </parameters> |
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410 | </action-factory> |
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411 | </extension> |
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412 | |
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413 | |
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414 | <extension |
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415 | id="net.sf.basedb.reggie.mbafplot-thumbnail-column" |
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416 | extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay" |
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417 | > |
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418 | <index>3</index> |
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419 | <about safe-scripts="1"> |
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420 | <name>mBAF plot</name> |
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421 | <description> |
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422 | Add a column to the list page of derived bioassays that display |
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423 | a thumbnail of the mBAF plot. |
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424 | </description> |
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425 | </about> |
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426 | <action-factory> |
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427 | <factory-class> |
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428 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
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429 | </factory-class> |
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430 | <parameters> |
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431 | <id>mbaf-plot</id> |
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432 | <title>mBAF plot</title> |
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433 | <link-name>mbaf_genotype.png</link-name> |
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434 | <subtype>ALIGNED_SEQUENCES</subtype> |
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435 | </parameters> |
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436 | </action-factory> |
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437 | </extension> |
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438 | |
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439 | |
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440 | <extension |
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441 | id="net.sf.basedb.reggie.libplate-column-derivedbioassay" |
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442 | extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay" |
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443 | > |
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444 | <index>2</index> |
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445 | <about safe-scripts="1"> |
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446 | <name>LibPlate</name> |
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447 | <description> |
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448 | Add a column to the list page of derived bioassays that display |
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449 | the name of the library plate (assumes that the extract that is |
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450 | linked is a library item). |
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451 | </description> |
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452 | </about> |
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453 | <action-factory> |
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454 | <factory-class> |
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455 | net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory |
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456 | </factory-class> |
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457 | <parameters> |
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458 | <id>extract.bioPlate</id> |
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459 | <title>LibPlate</title> |
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460 | <property>extract.bioWell.bioPlate</property> |
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461 | <filter-property>extract.bioWell.bioPlate.name</filter-property> |
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462 | <sort-property>extract.bioWell.bioPlate.name</sort-property> |
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463 | <valueType>STRING</valueType> |
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464 | <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class> |
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465 | <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class> |
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466 | </parameters> |
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467 | </action-factory> |
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468 | </extension> |
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469 | <extension |
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470 | id="net.sf.basedb.reggie.libplate-column-rawbioassay" |
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471 | extends="net.sf.basedb.clients.web.listcolumn.rawbioassay" |
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472 | > |
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473 | <index>2</index> |
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474 | <about safe-scripts="1"> |
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475 | <name>LibPlate</name> |
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476 | <description> |
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477 | Add a column to the list page of raw bioassays that display |
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478 | the name of the library plate (assumes that the extract that is |
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479 | linked is a library item). |
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480 | </description> |
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481 | </about> |
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482 | <action-factory> |
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483 | <factory-class> |
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484 | net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory |
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485 | </factory-class> |
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486 | <parameters> |
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487 | <id>parentExtract.bioPlate</id> |
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488 | <title>LibPlate</title> |
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489 | <property>parentExtract.bioWell.bioPlate</property> |
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490 | <filter-property>parentExtract.bioWell.bioPlate.name</filter-property> |
---|
491 | <sort-property>parentExtract.bioWell.bioPlate.name</sort-property> |
---|
492 | <valueType>STRING</valueType> |
---|
493 | <formatter-class>net.sf.basedb.reggie.extensions.LinkedItemFormatter</formatter-class> |
---|
494 | <export-formatter-class>net.sf.basedb.util.formatter.NameableFormatter</export-formatter-class> |
---|
495 | </parameters> |
---|
496 | </action-factory> |
---|
497 | </extension> |
---|
498 | <extension |
---|
499 | id="net.sf.basedb.reggie.histology-thumbnail-view" |
---|
500 | extends="net.sf.basedb.clients.web.toolbar.item.sample" |
---|
501 | > |
---|
502 | <index>3</index> |
---|
503 | <about safe-scripts="1"> |
---|
504 | <name>Stained image</name> |
---|
505 | <description> |
---|
506 | Add a thumbnail to the sample view page for stained |
---|
507 | histology samples that has a link to an image file. |
---|
508 | </description> |
---|
509 | </about> |
---|
510 | <action-factory> |
---|
511 | <factory-class> |
---|
512 | net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory |
---|
513 | </factory-class> |
---|
514 | <parameters> |
---|
515 | <link-name>image</link-name> |
---|
516 | <subtype>STAINED</subtype> |
---|
517 | </parameters> |
---|
518 | </action-factory> |
---|
519 | </extension> |
---|
520 | <extension |
---|
521 | id="net.sf.basedb.reggie.ndpi-thumbnail-view" |
---|
522 | extends="net.sf.basedb.clients.web.toolbar.item.bioplate" |
---|
523 | > |
---|
524 | <index>3</index> |
---|
525 | <about safe-scripts="1"> |
---|
526 | <name>NDPI image</name> |
---|
527 | <description> |
---|
528 | Add a thumbnail to the bioplate view page for HE glass |
---|
529 | has a link to an NDPI image file. |
---|
530 | </description> |
---|
531 | </about> |
---|
532 | <action-factory> |
---|
533 | <factory-class> |
---|
534 | net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory |
---|
535 | </factory-class> |
---|
536 | <parameters> |
---|
537 | <link-name>NDPI Image</link-name> |
---|
538 | <platetype>HE_GLASS</platetype> |
---|
539 | </parameters> |
---|
540 | </action-factory> |
---|
541 | </extension> |
---|
542 | <extension |
---|
543 | id="net.sf.basedb.reggie.genereport-thumbnail-view" |
---|
544 | extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay" |
---|
545 | > |
---|
546 | <index>3</index> |
---|
547 | <about safe-scripts="1"> |
---|
548 | <name>Gene report PDF</name> |
---|
549 | <description> |
---|
550 | Add a thumbnail to the raw bioassay view page for |
---|
551 | that has a link to "genereport.pdf". |
---|
552 | </description> |
---|
553 | </about> |
---|
554 | <action-factory> |
---|
555 | <factory-class> |
---|
556 | net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory |
---|
557 | </factory-class> |
---|
558 | <parameters> |
---|
559 | <link-name>genereport.pdf</link-name> |
---|
560 | <rawdatatype>CUFFLINKS</rawdatatype> |
---|
561 | </parameters> |
---|
562 | </action-factory> |
---|
563 | </extension> |
---|
564 | |
---|
565 | <extension |
---|
566 | id="net.sf.basedb.reggie.scanbreport-thumbnail-view" |
---|
567 | extends="net.sf.basedb.clients.web.toolbar.item.rawbioassay" |
---|
568 | > |
---|
569 | <index>3</index> |
---|
570 | <about safe-scripts="1"> |
---|
571 | <name>SCAN-B report PDF</name> |
---|
572 | <description> |
---|
573 | Add a thumbnail to the raw bioassay view page for |
---|
574 | that has a link to "scanbreport.pdf". |
---|
575 | </description> |
---|
576 | </about> |
---|
577 | <action-factory> |
---|
578 | <factory-class> |
---|
579 | net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory |
---|
580 | </factory-class> |
---|
581 | <parameters> |
---|
582 | <link-name>scanbreport.pdf</link-name> |
---|
583 | <rawdatatype>STRINGTIE</rawdatatype> |
---|
584 | </parameters> |
---|
585 | </action-factory> |
---|
586 | </extension> |
---|
587 | |
---|
588 | <extension |
---|
589 | id="net.sf.basedb.reggie.methylation-thumbnail-view" |
---|
590 | extends="net.sf.basedb.clients.web.toolbar.item.derivedbioassay" |
---|
591 | > |
---|
592 | <index>3</index> |
---|
593 | <about safe-scripts="1"> |
---|
594 | <name>Methylation beta adjustment plot</name> |
---|
595 | <description> |
---|
596 | Add a thumbnail to the Methylation derived bioassay |
---|
597 | view page that has a link to "adjustmentPlots.pdf". |
---|
598 | </description> |
---|
599 | </about> |
---|
600 | <action-factory> |
---|
601 | <factory-class> |
---|
602 | net.sf.basedb.reggie.extensions.ThumbnailsProxyFactory |
---|
603 | </factory-class> |
---|
604 | <parameters> |
---|
605 | <link-name>adjustmentPlots.pdf</link-name> |
---|
606 | <subtype>METHYLATION</subtype> |
---|
607 | </parameters> |
---|
608 | </action-factory> |
---|
609 | </extension> |
---|
610 | |
---|
611 | <extension |
---|
612 | id="net.sf.basedb.reggie.methylation-thumbnail-column" |
---|
613 | extends="net.sf.basedb.clients.web.listcolumn.derivedbioassay" |
---|
614 | > |
---|
615 | <index>3</index> |
---|
616 | <about safe-scripts="1"> |
---|
617 | <name>Methylation beta adjustment plot</name> |
---|
618 | <description> |
---|
619 | Add a column to the list page of derived bioassays that display |
---|
620 | a thumbnail of the Methylation beta adjustment plot. |
---|
621 | </description> |
---|
622 | </about> |
---|
623 | <action-factory> |
---|
624 | <factory-class> |
---|
625 | net.sf.basedb.reggie.extensions.ThumbnailsColumnFactory |
---|
626 | </factory-class> |
---|
627 | <parameters> |
---|
628 | <id>beta-plot</id> |
---|
629 | <title>Beta plot</title> |
---|
630 | <link-name>adjustmentPlots.pdf</link-name> |
---|
631 | <subtype>METHYLATION</subtype> |
---|
632 | </parameters> |
---|
633 | </action-factory> |
---|
634 | </extension> |
---|
635 | |
---|
636 | <extension |
---|
637 | id="net.sf.basedb.reggie.overview.case-summary" |
---|
638 | extends="net.sf.basedb.clients.web.overview.info-details" |
---|
639 | > |
---|
640 | <index>1</index> |
---|
641 | <about safe-scripts="1"> |
---|
642 | <name>Case overview</name> |
---|
643 | <description> |
---|
644 | Adds a section to the information pane in the "Item overview" |
---|
645 | functionality that display a link to the "Case summary" |
---|
646 | function in Reggie for all items that have a name pattern |
---|
647 | that starts with 7 digits. |
---|
648 | </description> |
---|
649 | </about> |
---|
650 | <action-factory> |
---|
651 | <factory-class> |
---|
652 | net.sf.basedb.reggie.extensions.CaseSummarySectionFactory |
---|
653 | </factory-class> |
---|
654 | <parameters> |
---|
655 | <id>reggie.case-summary</id> |
---|
656 | <title>Reggie</title> |
---|
657 | <include>~/reports/case_summary_hook.jsp</include> |
---|
658 | </parameters> |
---|
659 | </action-factory> |
---|
660 | </extension> |
---|
661 | |
---|
662 | <extension |
---|
663 | id="net.sf.basedb.reggie.toolbar.histology-score" |
---|
664 | extends="net.sf.basedb.clients.web.toolbar.item.bioplate" |
---|
665 | > |
---|
666 | <about safe-scripts="1"> |
---|
667 | <name>Histology score</name> |
---|
668 | <description> |
---|
669 | Adds a button to the toolbar of paraffin blocks and |
---|
670 | HE stain bioplates that start the 'histology scoring wizard'. |
---|
671 | </description> |
---|
672 | </about> |
---|
673 | <action-factory> |
---|
674 | <factory-class> |
---|
675 | net.sf.basedb.reggie.extensions.HistologyScoreButtonFactory |
---|
676 | </factory-class> |
---|
677 | <parameters> |
---|
678 | <title>Score HE glass</title> |
---|
679 | <clazz>button auto-init</clazz> |
---|
680 | <data-auto-init>reggie-he-score-link</data-auto-init> |
---|
681 | <data-home>$HOME$</data-home> |
---|
682 | <icon>~/images/microscope.png</icon> |
---|
683 | <script>~/scripts/he-score.js</script> |
---|
684 | </parameters> |
---|
685 | </action-factory> |
---|
686 | </extension> |
---|
687 | |
---|
688 | <extension |
---|
689 | id="net.sf.basedb.reggie.grid.job-complete" |
---|
690 | extends="net.sf.basedb.opengrid.job-complete" |
---|
691 | > |
---|
692 | <about> |
---|
693 | <name>Reggie job completion handler</name> |
---|
694 | <description> |
---|
695 | Handles completion of jobs started by Reggie. |
---|
696 | Depending on the job type it will typically initiate |
---|
697 | parsing of some result files, etc. |
---|
698 | </description> |
---|
699 | </about> |
---|
700 | <action-factory> |
---|
701 | <factory-class> |
---|
702 | net.sf.basedb.reggie.grid.JobCompletionHandlerFactory |
---|
703 | </factory-class> |
---|
704 | </action-factory> |
---|
705 | </extension> |
---|
706 | |
---|
707 | <extension |
---|
708 | id="net.sf.basedb.reggie.extensions.nextseq-signal" |
---|
709 | extends="net.sf.basedb.core.signal.job" |
---|
710 | > |
---|
711 | <about> |
---|
712 | <name>Reggie signal handler</name> |
---|
713 | <description> |
---|
714 | Responds to signals sent from BASE. Support |
---|
715 | for STATUS signal to get the progress of a |
---|
716 | NextSeq sequencing run. |
---|
717 | </description> |
---|
718 | </about> |
---|
719 | <action-factory> |
---|
720 | <factory-class> |
---|
721 | net.sf.basedb.reggie.extensions.ReggieSignalHandlerFactory |
---|
722 | </factory-class> |
---|
723 | </action-factory> |
---|
724 | </extension> |
---|
725 | |
---|
726 | <extension |
---|
727 | id="net.sf.basedb.reggie.auto-confirm-service" |
---|
728 | extends="net.sf.basedb.clients.web.services" |
---|
729 | > |
---|
730 | <about> |
---|
731 | <name>Reggie auto-confirm service</name> |
---|
732 | <description> |
---|
733 | A service that checks for secondary analysis |
---|
734 | items that has been flagged with AutoProcessing=AutoConfirm. |
---|
735 | If rules are met, the item is automatically |
---|
736 | confirmed and the next step in the analysis is started. |
---|
737 | </description> |
---|
738 | </about> |
---|
739 | <action-factory> |
---|
740 | <factory-class> |
---|
741 | net.sf.basedb.reggie.autoconfirm.AutoConfirmServiceFactory |
---|
742 | </factory-class> |
---|
743 | </action-factory> |
---|
744 | </extension> |
---|
745 | |
---|
746 | <extension |
---|
747 | id="net.sf.basedb.reggie.counter-service" |
---|
748 | extends="net.sf.basedb.clients.web.services" |
---|
749 | > |
---|
750 | <about> |
---|
751 | <name>Reggie counter service</name> |
---|
752 | <description> |
---|
753 | A service that count the number of items at |
---|
754 | various stages in the lab and analysis process. |
---|
755 | The counters are presented on the Reggie index page. |
---|
756 | If this service is stopped the counter will not |
---|
757 | be updated. |
---|
758 | </description> |
---|
759 | </about> |
---|
760 | <action-factory> |
---|
761 | <factory-class> |
---|
762 | net.sf.basedb.reggie.counter.CounterServiceFactory |
---|
763 | </factory-class> |
---|
764 | </action-factory> |
---|
765 | </extension> |
---|
766 | |
---|
767 | <extension |
---|
768 | id="net.sf.basedb.reggie.project-archive-service" |
---|
769 | extends="net.sf.basedb.clients.web.services" |
---|
770 | > |
---|
771 | <about> |
---|
772 | <name>Reggie project-archive file permission service</name> |
---|
773 | <description> |
---|
774 | Checks and manages file permissions in the project-archive |
---|
775 | based on the consent information on the related case. |
---|
776 | Files that belong to a case with Consent=Yes will get |
---|
777 | group-level read permission, all other files will get |
---|
778 | private permissions only. |
---|
779 | </description> |
---|
780 | </about> |
---|
781 | <action-factory> |
---|
782 | <factory-class> |
---|
783 | net.sf.basedb.reggie.projectarchive.ProjectArchiveServiceFactory |
---|
784 | </factory-class> |
---|
785 | </action-factory> |
---|
786 | </extension> |
---|
787 | |
---|
788 | <extension |
---|
789 | id="net.sf.basedb.reggie.vcf-actions" |
---|
790 | extends="net.sf.basedb.clients.web.file-viewer" |
---|
791 | > |
---|
792 | <about> |
---|
793 | <name>Genotype and variant call VCF viewer</name> |
---|
794 | <description> |
---|
795 | Add links for viewing the genotype QC VCF (qc_genotype.vcf) |
---|
796 | file and the filtered variant call VCF file (variants-filtered.vcf). |
---|
797 | </description> |
---|
798 | </about> |
---|
799 | <action-factory> |
---|
800 | <factory-class> |
---|
801 | net.sf.basedb.reggie.extensions.VcfViewerActionFactory |
---|
802 | </factory-class> |
---|
803 | <parameters> |
---|
804 | <script>~/scripts/vcf-actions.js</script> |
---|
805 | </parameters> |
---|
806 | </action-factory> |
---|
807 | </extension> |
---|
808 | |
---|
809 | <extension |
---|
810 | id="net.sf.basedb.reggie.toolbar.download-as-zip" |
---|
811 | extends="net.sf.basedb.clients.web.file-viewer" |
---|
812 | > |
---|
813 | <about safe-scripts="1"> |
---|
814 | <name>Download file as ZIP</name> |
---|
815 | <description> |
---|
816 | Implements an action that can be used on files to download |
---|
817 | them as a ZIP file. The ZIP file is created on the fly and |
---|
818 | has support for encryption with AES256. |
---|
819 | |
---|
820 | The action is currently only enabled CSV files inside |
---|
821 | the /home/SCANB/ReferralIdLogs directory. |
---|
822 | </description> |
---|
823 | </about> |
---|
824 | <action-factory> |
---|
825 | <factory-class> |
---|
826 | net.sf.basedb.reggie.extensions.DownloadAsZipActionFactory |
---|
827 | </factory-class> |
---|
828 | <parameters> |
---|
829 | <script>~/download-as-zip.js</script> |
---|
830 | </parameters> |
---|
831 | </action-factory> |
---|
832 | </extension> |
---|
833 | |
---|
834 | </extensions> |
---|