1 | <?xml version="1.0" encoding="UTF-8"?> |
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2 | <!DOCTYPE chapter PUBLIC |
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3 | "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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4 | "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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5 | <!-- |
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6 | $Id: import_export_data.xml 3246 2007-04-16 14:12:23Z martin $ |
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7 | |
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8 | Copyright (C) Authors contributing to this file. |
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9 | |
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10 | This file is part of BASE - BioArray Software Environment. |
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11 | Available at http://base.thep.lu.se/ |
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12 | |
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13 | BASE is free software; you can redistribute it and/or |
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14 | modify it under the terms of the GNU General Public License |
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15 | as published by the Free Software Foundation; either version 2 |
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16 | of the License, or (at your option) any later version. |
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17 | |
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18 | BASE is distributed in the hope that it will be useful, |
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19 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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20 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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21 | GNU General Public License for more details. |
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22 | |
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23 | You should have received a copy of the GNU General Public License |
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24 | along with this program; if not, write to the Free Software |
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25 | Foundation, Inc., 59 Temple Place - Suite 330, |
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26 | Boston, MA 02111-1307, USA. |
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27 | --> |
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28 | |
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29 | <chapter id="import_export_data"> |
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30 | <?dbhtml dir="import_export"?> |
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31 | <title>Import and export of data</title> |
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32 | <para> |
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33 | The data need first of all to be imported into the database before it can be used by/in the |
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34 | environment. The opposite is if the data should be used outside the environment, it then |
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35 | have to be exported before it can be used. These two actions, importing and exporting, are |
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36 | done through the plugin interface. |
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37 | </para> |
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38 | <para> |
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39 | Different kinds of import and export plugins, depending on the data, are used to get |
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40 | data/information in and out from the BASE 2's database. Some of the plugins can take, some |
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41 | even requires, a configuration to be able to run. If a plugin has configuration support or |
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42 | not, can be found at |
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43 | <menuchoice> |
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44 | <guimenu>Administrate</guimenu> |
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45 | <guimenuitem>Plugins</guimenuitem> |
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46 | <guisubmenu>Definitions</guisubmenu> |
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47 | </menuchoice> |
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48 | . The installation of BASE2 includes a collection of plugins, so called core plugins, and |
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49 | these are, like all other plugins, supervised by the administrator or an user with |
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50 | similar(at least write) permission on plugins. A list with these core plugins can be found |
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51 | on |
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52 | <ulink |
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53 | url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"> |
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54 | base2's homepage |
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55 | </ulink> |
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56 | . On this page are also configuration examples that can be downloaded for some of the |
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57 | plugins. |
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58 | </para> |
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59 | <para> |
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60 | If the |
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61 | <guibutton>Import</guibutton> |
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62 | or |
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63 | <guibutton>Export</guibutton> |
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64 | button is available in a page's toolbar the current context and item type is supported by at |
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65 | least one import and export plugins respectively that the logged in user has permission to |
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66 | use. |
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67 | </para> |
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68 | <note> |
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69 | <title>Missing/unavailable button</title> |
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70 | <para> |
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71 | The logged in user does usually not have enough permission on the expected plugin if the |
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72 | import- or export button is unavailable/not visible. Contact the administrator or |
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73 | similar user that has permission to administrate the plugins. |
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74 | </para> |
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75 | </note> |
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76 | <para> |
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77 | Following subsections contains information how to proceed when importing or exporting data |
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78 | in BASE2. |
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79 | </para> |
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80 | <sect1 id="import_export_data.import"> |
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81 | <title>Import</title> |
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82 | <para> |
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83 | Click on |
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84 | <guibutton>Import</guibutton> |
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85 | in the toolbar to import data into BASE2's database. This will open a pop-up window |
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86 | where the job, that shall perform the data import, can be configured. More about jobs |
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87 | and what a job is can be found under |
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88 | <xref linkend="jobs" /> |
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89 | . |
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90 | </para> |
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91 | |
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92 | <sect2 id="import_export_data.import.plugin_fileformat"> |
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93 | <title>Select plugin and file format</title> |
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94 | <helptext external_id="import.selectplugin" |
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95 | title="Select plugin and file format for data import"> |
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96 | <para> |
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97 | The first thing to do when configuring a job is to set which import plugin and |
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98 | file format to use alternatively let the interface choose suitable plugin/file |
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99 | format based on the file that shall be imported, more about this in |
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100 | <xref linkend="import_export_data.import.plugin_fileformat.autodetect" /> |
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101 | . |
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102 | </para> |
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103 | |
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104 | <sect3 id="import_export_data.import.plugin_fileformat.plugin"> |
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105 | <title>Plugin</title> |
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106 | <para> |
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107 | Available import plugins that the logged in user has permission to use and |
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108 | that support the current context are listed in the pop-up window's |
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109 | drop-down-list with plugins. Select the appropriate import plugin for the |
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110 | job from this list. At the bottom of the frame stands a short description |
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111 | about what the selected plugin does. More information about the plugins can |
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112 | be found under the menu choice |
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113 | <menuchoice> |
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114 | <guimenu>Administrate</guimenu> |
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115 | <guimenuitem>Plugins</guimenuitem> |
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116 | <guisubmenu>Definitions</guisubmenu> |
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117 | </menuchoice> |
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118 | </para> |
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119 | </sect3> |
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120 | |
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121 | <sect3 id="import_export_data.import.plugin_fileformat.fileformat"> |
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122 | <title>File format</title> |
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123 | <para> |
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124 | The drop down list with file format contains available file formats for the |
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125 | selected plugin. A file format configures a plugin how it should parse the |
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126 | file for importing it's data. Information about each file format can be |
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127 | found under the menu choice |
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128 | <menuchoice> |
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129 | <guimenu>Administrate</guimenu> |
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130 | <guimenuitem>Plugins</guimenuitem> |
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131 | <guisubmenu>Configurations</guisubmenu> |
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132 | </menuchoice> |
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133 | . Select the file format that should be used together with the plugin. |
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134 | </para> |
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135 | <para> |
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136 | Proceed to next window by clicking on |
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137 | <guibutton>Next</guibutton> |
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138 | </para> |
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139 | </sect3> |
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140 | |
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141 | <sect3 id="import_export_data.import.plugin_fileformat.autodetect"> |
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142 | <title>Auto detect</title> |
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143 | <para> |
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144 | Auto detect lets the BASE2 plugin-interface to choose plugin and/or file |
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145 | format by validating the data file that shall be imported. This option is |
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146 | set by default in both plugin- and file format drop-down lists when there is |
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147 | at least one plugin in the list that supports auto detection. |
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148 | </para> |
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149 | <note> |
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150 | <title>Support of auto detect</title> |
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151 | <para> |
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152 | Not all plugins support auto detection. The ones that do are marked in |
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153 | the drop down list with a |
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154 | <guilabel>X</guilabel> |
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155 | . |
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156 | </para> |
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157 | </note> |
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158 | <para> |
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159 | Set either both plugins and file formats or only file format to auto detect |
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160 | to use this feature. Click then on |
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161 | <guibutton>Next</guibutton> |
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162 | to go to the next window where the file to import from is selected. Press |
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163 | <guibutton>Browse…</guibutton> |
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164 | in this window to browse after the import file in the BASE2's file system. |
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165 | If the file doesn't exist in the file system it first has to be uploaded |
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166 | before it's possible to use it, read more about this under |
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167 | <xref linkend="file_system" /> |
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168 | . |
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169 | </para> |
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170 | <para> |
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171 | Proceed by clicking on |
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172 | <guibutton>Next</guibutton> |
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173 | . |
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174 | </para> |
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175 | <para> |
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176 | If there is a file format and a plugin compatible to the selected file, the |
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177 | next step will be to configure the job parameters. The file parameter is |
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178 | already set to the file that was selected earlier. Is there on the other |
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179 | hand no compatible file format or plugin that could be found there will be |
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180 | an error message that describes what went wrong. |
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181 | </para> |
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182 | <note> |
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183 | <title>More then one compatible plugin/file format</title> |
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184 | <para> |
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185 | The auto detect will pick the first plugin and file format it finds and |
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186 | it can therefore not be used if there are more then one plugin or file |
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187 | format that can import the selected file. |
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188 | </para> |
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189 | </note> |
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190 | </sect3> |
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191 | </helptext> |
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192 | </sect2> |
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193 | |
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194 | <sect2 id="import_export_data.import.jobparameters"> |
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195 | <title>Job parameters</title> |
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196 | <para> |
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197 | This window contains of a top line with the names of the selected plugin and |
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198 | configuration, a list with parameters to the left, area for input fields to the |
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199 | right and buttons to proceed with at the bottom. Which the parameters in the list |
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200 | are depends on the selected plugin and it's configuration. Common parameter for all |
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201 | import plugin is however the |
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202 | <guilabel>File</guilabel> |
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203 | parameter (already set if auto detect is used) which holds the file to import the |
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204 | data from. A click on a parameter in the list will display an input field and a |
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205 | description to the right of the list. Parameters that have a |
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206 | <guilabel>X</guilabel> |
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207 | in front of their names has already a value set and those parameters, which names |
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208 | are marked with a rectangle, are required and need to be set before it's possible to |
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209 | continuing with the job configuration. There will pop up a dialog window if not all |
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210 | required parameters had been set. |
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211 | </para> |
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212 | <para> |
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213 | Continue the job configuration by clicking on |
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214 | <guibutton>Next</guibutton> |
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215 | . In this window should information about the job be filled in, like name and |
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216 | description. Where name is required and need to have valid string as a value. There |
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217 | is also an option if the user want to get a message or not after the job is done. |
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218 | The check-box should be ticked if the owner of the job wants to get a message with a |
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219 | summary of the job's execution. |
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220 | </para> |
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221 | <para> |
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222 | Clicking on |
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223 | <guibutton>Finish</guibutton> |
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224 | when everything is set will end the job configuration and place the job in the BASE |
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225 | 2 server's job queue. A self-refreshing window appears with information about the |
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226 | job's status and execution time. How long time it takes before the job starts to run |
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227 | depends on which priority it and the other jobs in the queue have. The job doesn't |
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228 | dependent on the status window to be able to run and therefore can the window be |
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229 | closed without the execution is interrupted. |
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230 | </para> |
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231 | <tip> |
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232 | <title>View job status</title> |
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233 | <para> |
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234 | A job's status can be viewed at any time by opening it from the job list page, |
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235 | <menuchoice> |
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236 | <guimenuitem>View</guimenuitem> |
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237 | <guimenuitem>Jobs</guimenuitem> |
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238 | </menuchoice> |
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239 | . |
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240 | </para> |
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241 | </tip> |
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242 | </sect2> |
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243 | </sect1> |
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244 | |
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245 | <sect1 id="import_export_data.export"> |
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246 | <title>Export</title> |
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247 | <para> |
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248 | Before data from BASE 2's database can be used outside the program, it first had to be |
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249 | exported to a file which then can be downloaded to a local path from the BASE file |
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250 | system. |
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251 | </para> |
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252 | <para> |
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253 | A data export is done by a job that runs an export plugin for the current context. An |
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254 | export job is started by clicking on |
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255 | <guibutton>Export…</guibutton> |
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256 | in the toolbar, which will open a pop-up window where the job can be configured. |
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257 | </para> |
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258 | <helptext external_id="runplugin.selectplugin" title="Select plugin"> |
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259 | <para> |
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260 | The first thing in the configuration process is to choose which plugin the job |
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261 | should use and a plugin-configuration for those plugins that require it. More |
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262 | information about the plugins can be found in each plugin's documentation. |
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263 | </para> |
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264 | <variablelist> |
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265 | <title>Set plugin and configuration</title> |
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266 | <varlistentry> |
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267 | <term> |
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268 | <guilabel>Plugin</guilabel> |
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269 | </term> |
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270 | <listitem> |
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271 | <para> |
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272 | Select the plugin that shall do the export. Only plugins that are |
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273 | available for the logged in user and that supports the current item are |
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274 | in the drop down list. |
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275 | </para> |
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276 | </listitem> |
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277 | </varlistentry> |
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278 | <varlistentry> |
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279 | <term> |
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280 | <guilabel>Configuration</guilabel> |
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281 | </term> |
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282 | <listitem> |
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283 | <para> |
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284 | Select the configuration that should be used together with the plugin. |
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285 | Not all plugins supports configuration and this option is only visible |
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286 | if the selected plugin in |
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287 | <guilabel>Plugin</guilabel> |
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288 | has this support and visible configurations are those which can be used |
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289 | with the selected plugin above. More information about configuration |
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290 | support can be found for each plugin under. |
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291 | </para> |
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292 | </listitem> |
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293 | </varlistentry> |
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294 | </variablelist> |
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295 | <para> |
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296 | Click on |
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297 | <guibutton>Next</guibutton> |
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298 | to show the configuration of parameters for the job. |
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299 | </para> |
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300 | </helptext> |
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301 | <para> |
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302 | Common for all export plugins is the file parameter that decide where the export data |
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303 | should be saved. Some plugins support the option of download immediately which let the |
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304 | user to download the exported data to a local file system, by leaving the file parameter |
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305 | empty. For saving the exported data within the file system of BASE, it's recommended to |
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306 | use the |
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307 | <guibutton>Browse…</guibutton> |
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308 | button to get the right path and then complement it with the file's name. |
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309 | </para> |
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310 | <para> |
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311 | Click on |
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312 | <guibutton>Next</guibutton> |
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313 | to proceed to next configuration window. |
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314 | </para> |
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315 | <para> |
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316 | If the file parameter were left empty and immediately download was chosen the new window |
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317 | will have a |
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318 | <guibutton>Download</guibutton> |
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319 | button to specify where the data should be saved on the local computer. |
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320 | </para> |
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321 | <para> |
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322 | But if the file should be saved within the file system of BASE instead, there will be a |
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323 | window where the job should get a name and optionally a description. By then clicking on |
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324 | <guibutton>Finish</guibutton> |
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325 | the configuration process will end and the job will be put in the job queue. A |
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326 | self-refreshing window appears with information about the job's status and execution |
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327 | time. The job isn't dependent on the status window to run and it therefore be closed |
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328 | without interrupting the execution of the job. |
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329 | </para> |
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330 | <tip> |
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331 | <title>View job status</title> |
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332 | <para> |
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333 | A job's status can be viewed at any time by opening it from the job list page, |
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334 | <menuchoice> |
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335 | <guimenuitem>View</guimenuitem> |
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336 | <guimenuitem>Jobs</guimenuitem> |
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337 | </menuchoice> |
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338 | . |
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339 | </para> |
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340 | </tip> |
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341 | <sect2 id="import_export_data.export.table_export"> |
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342 | <title>Table export</title> |
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343 | <para> |
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344 | The table exporter is a common export plugin for all list pages in BASE 2 and it |
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345 | makes it possible for the user to export the list to either a XML-file or a |
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346 | tab-separated text file. The table exporter supports all list pages and is started, |
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347 | like the other export plugins, by clicking on |
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348 | <guibutton>Export…</guibutton> |
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349 | in the toolbar. |
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350 | </para> |
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351 | <sect3 id="import_export_data.export.table_export.configuration"> |
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352 | <title>Configuration</title> |
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353 | <para> |
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354 | Clicking on |
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355 | <guibutton>Export…</guibutton> |
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356 | will open a pop up window to configure the job in. If there are more plugins, |
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357 | that support the current context, then the table exporter the first thing will |
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358 | be to choose which plugin to use - in this case |
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359 | <guilabel>Table exporter</guilabel> |
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360 | . Confirm the choice and go to next window by clicking on |
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361 | <guibutton>Next</guibutton> |
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362 | . |
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363 | </para> |
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364 | <helptext external_id="simpleexport.options" title="Table-export options"> |
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365 | <para> |
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366 | In this window are the options set, which the table exporter should use when |
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367 | exporting the table. See the list below for more information about each |
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368 | option. |
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369 | <variablelist> |
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370 | <title>Export options</title> |
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371 | <varlistentry> |
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372 | <term> |
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373 | <guilabel>Format</guilabel> |
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374 | </term> |
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375 | <listitem> |
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376 | <para> |
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377 | The generated file can be either a tab-separated text file |
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378 | or a XML file. In the text file will the columns be tab |
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379 | separated and each row represent a row in the list. The |
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380 | XML-file option will generate a tag for each item and these |
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381 | will contain a child tag with property value for each |
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382 | selected column. |
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383 | </para> |
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384 | </listitem> |
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385 | </varlistentry> |
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386 | <varlistentry> |
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387 | <term> |
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388 | <guilabel>Which items?</guilabel> |
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389 | </term> |
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390 | <listitem> |
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391 | <para> |
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392 | This option decide which items that should be included in |
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393 | the exported data. |
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394 | <itemizedlist> |
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395 | <listitem> |
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396 | <para> |
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397 | Selected items(only available if items have been |
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398 | selected on the list page). Only selected items |
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399 | will be exported to the file. |
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400 | </para> |
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401 | </listitem> |
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402 | <listitem> |
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403 | <para> |
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404 | Current page. Exports all items viewed on the |
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405 | current list page. |
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406 | </para> |
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407 | </listitem> |
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408 | <listitem> |
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409 | <para> |
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410 | All pages. Items on all pages will be exported |
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411 | to the file. |
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412 | </para> |
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413 | </listitem> |
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414 | </itemizedlist> |
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415 | </para> |
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416 | </listitem> |
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417 | </varlistentry> |
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418 | <varlistentry> |
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419 | <term> |
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420 | <guilabel>Which columns?</guilabel> |
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421 | </term> |
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422 | <listitem> |
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423 | <para> |
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424 | Names of those columns that should be included in the export |
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425 | should be listed in the left list-box. A column name is |
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426 | moved to the other list-box by first marking it and then |
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427 | clicking on one of the buttons located between the |
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428 | list-boxes. |
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429 | </para> |
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430 | <para> |
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431 | The order in which the columns should be exported in can be |
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432 | changed with the buttons to the left of the list. Simply |
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433 | mark a name of a column and click on the buttons to move the |
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434 | name either up or down in the list. |
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435 | </para> |
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436 | <tip> |
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437 | <title>Using presets</title> |
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438 | <para> |
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439 | Use the drop down list of presets, located under the |
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440 | option name, to easily get predefined or own presets of |
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441 | column settings. |
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442 | </para> |
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443 | </tip> |
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444 | </listitem> |
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445 | </varlistentry> |
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446 | <varlistentry> |
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447 | <term> |
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448 | <guilabel>Save as</guilabel> |
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449 | </term> |
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450 | <listitem> |
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451 | <para> |
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452 | The last option is where the file with the exported data |
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453 | should be saved. Leave the text field empty if the file is |
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454 | to be downloaded immediately or enter a path within base2's |
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455 | file system to store the file on the server. Check |
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456 | <guilabel>Overwrite existing file</guilabel> |
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457 | if an already existing file with the same name should be |
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458 | overwritten. Click on |
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459 | <guibutton>Ok</guibutton> |
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460 | to proceed when all options have been set for the export. |
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461 | </para> |
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462 | </listitem> |
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463 | </varlistentry> |
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464 | </variablelist> |
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465 | </para> |
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466 | </helptext> |
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467 | <para> |
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468 | The rest of the configuration process is the same as for all the other export |
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469 | plugins. |
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470 | </para> |
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471 | </sect3> |
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472 | </sect2> |
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473 | </sect1> |
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474 | </chapter> |
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