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: file_system.xml 3242 2007-04-13 12:56:43Z 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="file_system"> |
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30 | <!-- <?dbhtml dir="filesystem"?> --> |
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31 | <title>File management</title> |
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32 | <sect1 id="file_system.system"> |
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33 | <title>File system</title> |
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34 | <para> |
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35 | Files in BASE2 are managed from the page at |
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36 | <menuchoice> |
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37 | <guimenu>View</guimenu> |
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38 | <guimenuitem>Files</guimenuitem> |
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39 | </menuchoice> |
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40 | . The basic layout on the page is the same as for all the other list pages in BASE2 but |
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41 | there are some differences e.g. there is a navigation tree to the left, used to browse |
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42 | the directory structure, and there are some buttons in the toolbar, that are special for |
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43 | files and directories. The figure below is a representation of the files and |
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44 | directories-page and is followed with a short description to some of the special |
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45 | functions. |
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46 | </para> |
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47 | <figure id="file.system.figures.filepage"> |
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48 | <title>The file page</title> |
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49 | <screenshot> |
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50 | <mediaobject> |
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51 | <imageobject> |
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52 | <imagedata fileref="figures/filepage.png" format="PNG" /> |
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53 | </imageobject> |
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54 | </mediaobject> |
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55 | </screenshot> |
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56 | </figure> |
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57 | <variablelist> |
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58 | <varlistentry> |
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59 | <term> |
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60 | <interface>1. Home directory for current user</interface> |
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61 | </term> |
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62 | <listitem> |
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63 | <para> |
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64 | This is the logged in user's home directory with sub directories. It is |
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65 | visible if current user has a home directory and is then always located at |
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66 | the top of the navigation tree. More about this can be read in |
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67 | <xref linkend="file_system.system.browse.tree.home" /> |
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68 | </para> |
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69 | </listitem> |
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70 | </varlistentry> |
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71 | |
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72 | <varlistentry> |
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73 | <term> |
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74 | <interface>2. Other users</interface> |
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75 | </term> |
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76 | <listitem> |
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77 | <para> |
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78 | The other users' home directories that the current user has read permission |
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79 | on are listed here, including his/her own. |
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80 | </para> |
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81 | </listitem> |
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82 | </varlistentry> |
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83 | |
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84 | <varlistentry> |
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85 | <term> |
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86 | <interface>3. Refresh button</interface> |
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87 | </term> |
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88 | <listitem> |
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89 | <para> |
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90 | This button, which is located at the bottom of the navigation tree, |
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91 | refreshes/updates the directory tree. It can for example be used to get a |
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92 | recently created directory to appear in the tree. |
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93 | </para> |
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94 | </listitem> |
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95 | </varlistentry> |
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96 | |
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97 | <varlistentry> |
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98 | <term> |
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99 | <interface>4. Current directory</interface> |
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100 | </term> |
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101 | <listitem> |
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102 | <para>Shows the full BASE2-path to current directory.</para> |
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103 | </listitem> |
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104 | </varlistentry> |
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105 | |
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106 | <varlistentry> |
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107 | <term> |
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108 | <interface>5. View a file's contents</interface> |
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109 | </term> |
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110 | <listitem> |
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111 | <para> |
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112 | A click on this icon will open the file's contents in a new window. If the |
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113 | browser doesn't has support to view the file there will be a dialog window |
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114 | to download the file instead. |
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115 | </para> |
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116 | </listitem> |
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117 | </varlistentry> |
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118 | |
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119 | <varlistentry> |
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120 | <term> |
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121 | <interface>6. Download file</interface> |
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122 | </term> |
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123 | <listitem> |
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124 | <para> |
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125 | Download the file to a local computer with this icon. The download will |
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126 | start in a new dialog window. |
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127 | </para> |
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128 | </listitem> |
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129 | </varlistentry> |
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130 | |
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131 | <varlistentry> |
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132 | <term> |
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133 | <interface>7. Re-upload a file</interface> |
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134 | </term> |
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135 | <listitem> |
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136 | <para> |
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137 | This icon is only visible for those files that have been moved offline and |
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138 | it can be used to re-upload the file into BASE2's file system. Start to |
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139 | upload the file to the same position by clicking on the icon. |
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140 | </para> |
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141 | </listitem> |
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142 | </varlistentry> |
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143 | |
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144 | <varlistentry> |
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145 | <term> |
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146 | <interface>8. Contents in current directory</interface> |
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147 | </term> |
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148 | <listitem> |
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149 | <para> |
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150 | This area contains files and sub directories that are located in the current |
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151 | directory in the navigation tree. |
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152 | </para> |
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153 | </listitem> |
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154 | </varlistentry> |
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155 | |
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156 | <varlistentry> |
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157 | <term> |
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158 | <interface>9. Navigation tree</interface> |
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159 | </term> |
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160 | <listitem> |
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161 | <para> |
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162 | This sidebar displays the tree of directories that the current user has |
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163 | permission to read. Click on a directory to display it's contents in the |
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164 | list or click on the plus sign to the left to expand directory and view the |
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165 | sub directories (no plus sign - no sub directories). |
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166 | </para> |
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167 | </listitem> |
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168 | </varlistentry> |
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169 | </variablelist> |
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170 | |
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171 | <sect2 id="file_system.system.browse"> |
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172 | <title>Browse the file system</title> |
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173 | <para> |
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174 | Browsing BASE2's file system is done from the navigation bar by clicking on a |
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175 | directory in the tree to view it's contents. Both sub directories and files in the |
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176 | selected directory are showed. A directory with sub directories can be expand with a |
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177 | click on the plus-sign. |
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178 | </para> |
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179 | <note> |
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180 | <title>Browse a directory</title> |
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181 | <para> |
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182 | A directory can only be open from the navigation tree and never from the list. A |
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183 | click on a directory's name in the list will open the directory's edit window. |
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184 | </para> |
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185 | </note> |
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186 | <sect3 id="file_system.system.browse.tree"> |
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187 | <title>Navigation tree</title> |
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188 | <para> |
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189 | The navigation tree contains of folders/directories that the logged in user has |
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190 | permission to read. At the top is the current user's home directory and under it |
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191 | is a folder with all accessible home directories. |
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192 | </para> |
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193 | <para> |
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194 | The tree can be updated with the refresh-button at the bottom of the panel (the |
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195 | tree isn't self-refreshing). |
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196 | </para> |
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197 | <sect4 id="file_system.system.browse.tree.home"> |
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198 | <title>Home directory - 'My home'</title> |
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199 | <para> |
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200 | To make it easier for the logged in user to find his/her directory without |
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201 | having to scroll through the whole list of home directories, his or hers |
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202 | home directory is located at the top of the navigation tree under the |
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203 | <interface>My home</interface> |
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204 | folder . |
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205 | </para> |
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206 | <note> |
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207 | <title>No home directory</title> |
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208 | <para> |
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209 | Not all users have a home directory connected to their accounts. If |
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210 | <interface>My home</interface> |
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211 | is missing, it most certainly depends on that the current user account |
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212 | haven't got a home directory. Home directories are managed by the user |
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213 | administrator on the BASE2 server. |
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214 | </para> |
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215 | </note> |
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216 | </sect4> |
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217 | </sect3> |
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218 | </sect2> |
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219 | <sect2 id="file_system.system.qouta"> |
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220 | <title>Disk space quota</title> |
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221 | <para> |
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222 | Normally the user accounts is assigned with limited quota of disk space used to |
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223 | store files, raw data or experiments on. The three categories have, in case of disk |
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224 | quota, a total limit of space to use and it's also possible for them to have a limit |
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225 | by their own too. |
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226 | <example> |
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227 | <title>Disk quota</title> |
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228 | <para> |
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229 | The user account has a total quota of 1GB but there is also a limitation of |
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230 | raw data to be at maximum 500MB. This will prevent the raw data to take more |
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231 | then 500 MB of the total quota. |
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232 | </para> |
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233 | </example> |
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234 | More information about how much quota the current account has and how much of it |
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235 | that is occupied can be found at the account's home page, described in |
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236 | <xref linkend="webclient.intro.homepage" /> |
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237 | . |
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238 | </para> |
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239 | </sect2> |
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240 | </sect1> |
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241 | |
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242 | <sect1 id="file_system.handling"> |
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243 | <title>Handling files</title> |
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244 | <para></para> |
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245 | <sect2 id="file_system.handling.upload"> |
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246 | <title>Upload a file</title> |
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247 | <para> |
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248 | Uploading a file is started clicking on |
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249 | <guibutton>Upload file…</guibutton> |
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250 | in the toolbar. The uploaded file will be placed in current directory. |
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251 | </para> |
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252 | <helptext external_id="file.upload" title="Upload a file"> |
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253 | <para> |
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254 | A couple of parameters need to be configured before uploading the file. |
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255 | <variablelist> |
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256 | <title>Parameters</title> |
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257 | <varlistentry> |
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258 | <term> |
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259 | <guilabel>Directory</guilabel> |
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260 | </term> |
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261 | <listitem> |
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262 | <para> |
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263 | Shows the current directory, where the file will be uploaded. |
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264 | This property can't be changed and is only for information. |
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265 | </para> |
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266 | </listitem> |
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267 | </varlistentry> |
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268 | <varlistentry> |
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269 | <term> |
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270 | <guilabel>File</guilabel> |
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271 | </term> |
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272 | <listitem> |
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273 | <para> |
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274 | This field is required and needs to have a valid file path for |
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275 | the local computer before the upload is started. Use |
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276 | <guibutton>Browse…</guibutton> |
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277 | to choose which file to upload. |
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278 | </para> |
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279 | </listitem> |
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280 | </varlistentry> |
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281 | <varlistentry> |
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282 | <term> |
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283 | <guilabel>Type</guilabel> |
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284 | </term> |
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285 | <listitem> |
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286 | <para> |
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287 | This is the file-type that the uploaded file should get. The |
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288 | file-types to choose between from the drop-down list are |
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289 | described in |
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290 | <xref linkend="file_system.filetypes" /> |
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291 | . Select |
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292 | <userinput>- none -</userinput> |
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293 | if the file shouldn't be associated with any BASE2 file type. |
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294 | </para> |
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295 | </listitem> |
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296 | </varlistentry> |
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297 | <varlistentry> |
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298 | <term> |
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299 | <guilabel>Description</guilabel> |
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300 | </term> |
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301 | <listitem> |
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302 | <para> |
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303 | A description about the uploaded file can be put into this text |
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304 | area. Use the magnifying glass to edit the text in a pop-up |
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305 | window with a larger text area. |
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306 | </para> |
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307 | </listitem> |
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308 | </varlistentry> |
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309 | <varlistentry> |
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310 | <term> |
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311 | <guilabel>Max transfer rate</guilabel> |
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312 | </term> |
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313 | <listitem> |
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314 | <para> |
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315 | This shows the maximum transfer rate that the upload will |
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316 | approximately reach. It's not editable. |
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317 | </para> |
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318 | </listitem> |
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319 | </varlistentry> |
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320 | <varlistentry> |
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321 | <term> |
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322 | <guilabel>Compressed file</guilabel> |
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323 | </term> |
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324 | <listitem> |
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325 | <para> |
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326 | These settings only intends zip-files or other compressed files. |
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327 | <variablelist> |
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328 | <varlistentry> |
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329 | <term>File extension</term> |
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330 | <listitem> |
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331 | <para> |
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332 | The kind of compressed file that is selected in |
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333 | <guilabel>File</guilabel> |
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334 | . |
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335 | </para> |
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336 | </listitem> |
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337 | </varlistentry> |
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338 | <varlistentry> |
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339 | <term>Unpack file</term> |
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340 | <listitem> |
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341 | <para> |
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342 | Tick off this box if the compressed file should |
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343 | be unpacked after it had been uploaded. |
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344 | </para> |
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345 | </listitem> |
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346 | </varlistentry> |
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347 | <varlistentry> |
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348 | <term>Overwrite existing files</term> |
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349 | <listitem> |
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350 | <para> |
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351 | This check-box is only available when the |
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352 | uploaded file should be unpacked. It should be |
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353 | ticked off if any existing files with the same |
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354 | name should be overwritten when unpacking the |
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355 | uploaded compressed file. |
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356 | </para> |
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357 | </listitem> |
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358 | </varlistentry> |
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359 | <varlistentry> |
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360 | <term>Keep the compressed file</term> |
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361 | <listitem> |
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362 | <para> |
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363 | This check-box is only available when the |
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364 | uploaded file should be unpacked. Use this |
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365 | check-box if the compressed file should be kept |
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366 | after it has been unpacked. |
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367 | </para> |
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368 | </listitem> |
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369 | </varlistentry> |
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370 | </variablelist> |
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371 | </para> |
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372 | </listitem> |
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373 | </varlistentry> |
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374 | </variablelist> |
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375 | </para> |
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376 | <para> |
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377 | Finish the configuration by clicking on either |
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378 | <guibutton>Upload</guibutton> |
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379 | , which will start uploading the selected file, or |
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380 | <guibutton>Cancel</guibutton> |
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381 | to abort the upload procedure. |
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382 | </para> |
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383 | </helptext> |
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384 | </sect2> |
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385 | <sect2 id="file_system.handling.edit"> |
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386 | <title>Edit a file</title> |
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387 | <para> |
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388 | The edit window to set a file's property in can either be open with |
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389 | <guibutton>Edit…</guibutton> |
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390 | that is located in the toolbar at the file's view page or by holding down |
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391 | <keycap>ctrl</keycap> |
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392 | , |
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393 | <keycap>alt</keycap> |
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394 | or |
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395 | <keycap>shift</keycap> |
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396 | when clicking on the file's name in the list. It requires that the current user has |
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397 | write permission on the file to be able to edit and set the properties. |
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398 | </para> |
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399 | |
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400 | <helptext external_id="file.edit" title="Edit file properties"> |
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401 | <variablelist> |
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402 | <title>Properties</title> |
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403 | <para> |
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404 | These are the file's properties that are displayed in the pop-up window. |
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405 | </para> |
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406 | <varlistentry> |
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407 | <term> |
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408 | <guilabel>Path</guilabel> |
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409 | </term> |
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410 | <listitem> |
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411 | <para> |
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412 | This is the path where the file is located. This can only be changed |
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413 | by moving the file, read more about how this is done in |
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414 | <xref linkend="file_system.handling.move" /> |
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415 | . |
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416 | </para> |
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417 | </listitem> |
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418 | </varlistentry> |
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419 | <varlistentry> |
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420 | <term> |
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421 | <guilabel>Name</guilabel> |
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422 | </term> |
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423 | <listitem> |
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424 | <para> |
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425 | The file's name, which can't be left empty and must be unique in |
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426 | current directory. The maximum length of the file name is 255 |
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427 | characters and it can contain blank spaces but not any of |
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428 | <keycap>~</keycap> |
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429 | , |
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430 | <keycap>\</keycap> |
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431 | , |
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432 | <keycap>/</keycap> |
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433 | , |
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434 | <keycap>:</keycap> |
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435 | , |
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436 | <keycap>;</keycap> |
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437 | , |
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438 | <keycap>*</keycap> |
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439 | , |
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440 | <keycap>?</keycap> |
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441 | , |
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442 | <keycap><</keycap> |
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443 | , |
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444 | <keycap>></keycap> |
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445 | or |
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446 | <keycap>|</keycap> |
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447 | . |
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448 | </para> |
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449 | </listitem> |
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450 | </varlistentry> |
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451 | <varlistentry> |
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452 | <term> |
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453 | <guilabel>Type</guilabel> |
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454 | </term> |
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455 | <listitem> |
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456 | <para> |
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457 | Sets which kind of type the file is. Select the file type to use |
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458 | from the drop down list with available types. The option |
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459 | <guilabel>-none-</guilabel> |
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460 | should be used if the file shouldn't be associated with any kind of |
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461 | file type. |
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462 | </para> |
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463 | </listitem> |
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464 | </varlistentry> |
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465 | <varlistentry> |
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466 | <term> |
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467 | <guilabel>MIME type</guilabel> |
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468 | </term> |
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469 | <listitem> |
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470 | <para> |
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471 | The file's content/media type. This is normally set automatically |
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472 | when uploading the file into BASE2 but it can be changed by an user, |
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473 | that has write permissions, at any time. |
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474 | </para> |
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475 | </listitem> |
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476 | </varlistentry> |
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477 | <varlistentry> |
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478 | <term> |
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479 | <guilabel>Description</guilabel> |
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480 | </term> |
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481 | <listitem> |
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482 | <para> |
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483 | This text area can be used to store relevant information about file |
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484 | and it's contents. Use the magnifying glass, located to the right |
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485 | under the text area, to edit the text in a larger window. |
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486 | </para> |
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487 | </listitem> |
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488 | </varlistentry> |
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489 | </variablelist> |
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490 | <para> |
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491 | Finish the editing process by pressing either |
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492 | <guibutton>Save</guibutton> |
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493 | to save the properties to the database or |
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494 | <guibutton>Cancel</guibutton> |
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495 | to abort and discard the changes. |
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496 | </para> |
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497 | </helptext> |
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498 | |
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499 | </sect2> |
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500 | <sect2 id="file_system.handling.remove"> |
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501 | <title>Delete, restore and move offline</title> |
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502 | <para> |
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503 | These functions are used to manage the directories and files' existence on the |
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504 | server, to keep the list of files and directories up-to-date and release disk space |
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505 | on server. |
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506 | </para> |
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507 | <sect3 id="file_system.handling.remove.delete"> |
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508 | <title>Delete</title> |
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509 | <para> |
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510 | A deleted file/directory is moved to the account's trash can and is marked to be |
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511 | removed. Those items that have been marked as deleted can't be used in analysis |
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512 | or other activities in BASE2 but they are not removed from the server and can be |
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513 | restored again by the users that have write permission on the items. |
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514 | </para> |
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515 | <para> |
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516 | Before a file or directory can be deleted it first has to be selected, this is |
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517 | done by ticking off the check-box in front of it's name in list. Click then on |
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518 | <guibutton>Delete</guibutton> |
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519 | to mark the item as deleted. |
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520 | </para> |
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521 | <tip> |
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522 | <title>Delete many directories/files</title> |
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523 | <para> |
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524 | Select all those items, that should be deleted in a list to flag them all |
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525 | for deletion at the same time. |
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526 | </para> |
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527 | </tip> |
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528 | <para> |
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529 | Files and directories that are marked for deletion can be included in the list |
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530 | by selecting |
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531 | <guilabel>Removed</guilabel> |
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532 | from the drop-down list with presets, see |
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533 | <xref linkend="webclient.figures.viewpresets" /> |
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534 | .Those which have been deleted are marked with a trash can icon in front of |
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535 | their names. |
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536 | </para> |
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537 | </sect3> |
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538 | <sect3 id="file_system.handling.remove.restore"> |
---|
539 | <title>Restore</title> |
---|
540 | <para> |
---|
541 | Files and directories that have been marked for deletion, and not yet removed |
---|
542 | from the trash can, can be restored again without any loss of information. To do |
---|
543 | that, the removed items have to be made visible in the list and which is done by |
---|
544 | selecting |
---|
545 | <guilabel>Removed</guilabel> |
---|
546 | in the drop down list of presets, see |
---|
547 | <xref linkend="webclient.figures.viewpresets" /> |
---|
548 | . |
---|
549 | </para> |
---|
550 | <para> |
---|
551 | Select the file or directory that should be restored, by ticking the check box |
---|
552 | to the left of the item. Then click on |
---|
553 | <guibutton>Restore</guibutton> |
---|
554 | in the toolbar to restore and remove the deletion flag. The trash can has now |
---|
555 | disappeared in front of the item that was restored and it's possible to use the |
---|
556 | item in BASE2 again. |
---|
557 | </para> |
---|
558 | <tip> |
---|
559 | <title>Restoring multiple directories/files</title> |
---|
560 | <para> |
---|
561 | Multiple files and directories can be restored at the same time. This is |
---|
562 | done by selecting all the items that should be restored before pressing the |
---|
563 | restore button. |
---|
564 | </para> |
---|
565 | </tip> |
---|
566 | </sect3> |
---|
567 | <sect3 id="file_system.handling.remove.move_offline"> |
---|
568 | <title>Move offline</title> |
---|
569 | <para> |
---|
570 | Moving a file offline means that the physical file is deleted from the server's |
---|
571 | disk space but the file will still exist as an item in the database. This makes |
---|
572 | it possible to save disk space but still be able to associated the file with |
---|
573 | other items in BASE2. |
---|
574 | </para> |
---|
575 | <para> |
---|
576 | Tick the check-box for those files that should be moved offline and press then |
---|
577 | <menuchoice> |
---|
578 | <guibutton>Move…</guibutton> |
---|
579 | <guisubmenu>Offline…</guisubmenu> |
---|
580 | </menuchoice> |
---|
581 | in the toolbar . The selected files will be moved immediately and disk space |
---|
582 | will be released. |
---|
583 | </para> |
---|
584 | </sect3> |
---|
585 | </sect2> |
---|
586 | <sect2 id="file_system.handling.actions"> |
---|
587 | <title>Actions</title> |
---|
588 | <para> |
---|
589 | Actions is a separate column in the list with files and sub directories. In this |
---|
590 | column are a couple of icons to click on to perform different kinds of actions on a |
---|
591 | file, like downloading the file, viewing the file or upload a file that has been |
---|
592 | moved offline. Each one of these actions are described below. |
---|
593 | </para> |
---|
594 | <sect3 id="file_system.handling.actions.download"> |
---|
595 | <title>Download</title> |
---|
596 | <para> |
---|
597 | This will let the user to download the contents of a file to a path on a local |
---|
598 | computer. The window that opens contains the selected file's name, size e.t.c. |
---|
599 | and it will also open a download dialog window where the user can choose what to |
---|
600 | do with the file locally. |
---|
601 | <tip> |
---|
602 | <title>Download doesn't start</title> |
---|
603 | <para> |
---|
604 | Click on the file's path name in the pop-up window if the download |
---|
605 | dialog window doesn't appears. |
---|
606 | </para> |
---|
607 | </tip> |
---|
608 | </para> |
---|
609 | <para> |
---|
610 | Close the pop-up window and return to file page with |
---|
611 | <guibutton>Close</guibutton> |
---|
612 | </para> |
---|
613 | </sect3> |
---|
614 | <sect3 id="file_system.handling.actions.view"> |
---|
615 | <title>View contents of file</title> |
---|
616 | <para> |
---|
617 | A file's contents can be displayed directly in the web browser if current |
---|
618 | browser supports the file's miame type. Click on the icon to view the contents |
---|
619 | in a new window. If the miame-type isn't supported by the browser there will be |
---|
620 | a dialog-window to download the file with instead. |
---|
621 | </para> |
---|
622 | </sect3> |
---|
623 | <sect3 id="file_system.handling.actions.reupload"> |
---|
624 | <title>Re-upload a file</title> |
---|
625 | <para> |
---|
626 | A file that has been moved offline can be uploaded again by clicking on the icon |
---|
627 | in the actions-column, see number 7 in |
---|
628 | <xref linkend="file.system.figures.filepage" /> |
---|
629 | . The procedure to upload the file is the same as described in |
---|
630 | <xref linkend="file_system.handling.upload" /> |
---|
631 | <important> |
---|
632 | <para> |
---|
633 | There is no check to confirm that the file that is going to be uploaded |
---|
634 | is the same that was originally stored in BASE2. |
---|
635 | </para> |
---|
636 | </important> |
---|
637 | </para> |
---|
638 | </sect3> |
---|
639 | </sect2> |
---|
640 | <sect2 id="file_system.handling.directories"> |
---|
641 | <title>Directories</title> |
---|
642 | <para> |
---|
643 | Directories in BASE2 are folders where files can be organized into. Click on |
---|
644 | <guibutton>New directory…</guibutton> |
---|
645 | in the toolbar to create a directory in current path and edit the properties as |
---|
646 | described below. |
---|
647 | </para> |
---|
648 | <sect3 id="file_system.handling.directories.edit"> |
---|
649 | <title>Edit a directory</title> |
---|
650 | <para> |
---|
651 | The window to edit a directory's properties is opened either by clicking on the |
---|
652 | directory's name in the list or when creating a new directory. |
---|
653 | </para> |
---|
654 | <helptext external_id="directory.edit" title="Edit directory"> |
---|
655 | <para> |
---|
656 | <variablelist> |
---|
657 | <title>Properties</title> |
---|
658 | <varlistentry> |
---|
659 | <term> |
---|
660 | <guilabel>Path</guilabel> |
---|
661 | </term> |
---|
662 | <listitem> |
---|
663 | <para> |
---|
664 | This property is read-only in the edit window but can be |
---|
665 | change instead by moving the directory, described in |
---|
666 | <xref linkend="file_system.handling.move" /> |
---|
667 | </para> |
---|
668 | </listitem> |
---|
669 | </varlistentry> |
---|
670 | <varlistentry> |
---|
671 | <term> |
---|
672 | <guilabel>Name</guilabel> |
---|
673 | </term> |
---|
674 | <listitem> |
---|
675 | <para> |
---|
676 | The directory's name to identify it with in the list. This |
---|
677 | field must have a value and it has to be an unique name for |
---|
678 | the current directory. |
---|
679 | </para> |
---|
680 | </listitem> |
---|
681 | </varlistentry> |
---|
682 | <varlistentry> |
---|
683 | <term> |
---|
684 | <guilabel>Description</guilabel> |
---|
685 | </term> |
---|
686 | <listitem> |
---|
687 | <para> |
---|
688 | Any relevant information about the directory can be written |
---|
689 | in this text area. The magnifying glass down to the right |
---|
690 | can be used to edit the description text in a larger text |
---|
691 | area, just click on the icon to open it in a separate pop-up |
---|
692 | window. |
---|
693 | </para> |
---|
694 | </listitem> |
---|
695 | </varlistentry> |
---|
696 | </variablelist> |
---|
697 | </para> |
---|
698 | <para> |
---|
699 | The editing process is completed with either |
---|
700 | <guibutton>Save</guibutton> |
---|
701 | , to save the properties into the database, or with |
---|
702 | <guibutton>Cancel</guibutton> |
---|
703 | to discard the changes. Both of the buttons will close the edit window and |
---|
704 | if the directory is updated the list will be reloaded with the directory's |
---|
705 | new properties. |
---|
706 | </para> |
---|
707 | </helptext> |
---|
708 | </sect3> |
---|
709 | </sect2> |
---|
710 | <sect2 id="file_system.handling.move"> |
---|
711 | <title>Move file/directory</title> |
---|
712 | <para> |
---|
713 | Files and directories can be moved to other directories for re-organization. The |
---|
714 | user need to have write permission on the target directory to be able to move the |
---|
715 | files/directories to it. |
---|
716 | </para> |
---|
717 | <para> |
---|
718 | Select first of all those files and directories in current path that should be moved |
---|
719 | and click then on |
---|
720 | <menuchoice> |
---|
721 | <guibutton>Move…</guibutton> |
---|
722 | <guisubmenu>To another directory</guisubmenu> |
---|
723 | </menuchoice> |
---|
724 | in the toolbar to open a window with the directory tree where the target directory |
---|
725 | can be picked. |
---|
726 | </para> |
---|
727 | <para> |
---|
728 | Choose a directory where the selected items should be moved to. Doesn't the |
---|
729 | directory exist, it can be created in the pop-up window's current path, with |
---|
730 | <guibutton>New…</guibutton> |
---|
731 | . |
---|
732 | </para> |
---|
733 | <para> |
---|
734 | Click on |
---|
735 | <guibutton>Ok</guibutton> |
---|
736 | to carry out the move or |
---|
737 | <guibutton>Cancel</guibutton> |
---|
738 | to abort. |
---|
739 | </para> |
---|
740 | </sect2> |
---|
741 | </sect1> |
---|
742 | |
---|
743 | <sect1 id="file_system.filetypes"> |
---|
744 | <title>File types</title> |
---|
745 | <para> |
---|
746 | A file can be associated with one of the file types that exists in BASE2. File types |
---|
747 | make it possible to sort the files depending of what kind of file it is. |
---|
748 | </para> |
---|
749 | <variablelist> |
---|
750 | <title>File types</title> |
---|
751 | <para>Following file types exists in BASE2.</para> |
---|
752 | <varlistentry> |
---|
753 | <term>Image</term> |
---|
754 | <listitem> |
---|
755 | <para>Indicates that the file is an image file.</para> |
---|
756 | </listitem> |
---|
757 | </varlistentry> |
---|
758 | <varlistentry> |
---|
759 | <term>Plate</term> |
---|
760 | <listitem> |
---|
761 | <para>The associated file is a file with information about plate/plates.</para> |
---|
762 | </listitem> |
---|
763 | </varlistentry> |
---|
764 | <varlistentry> |
---|
765 | <term>Plate mapping</term> |
---|
766 | <listitem> |
---|
767 | <para>Files with information about plate mapping.</para> |
---|
768 | </listitem> |
---|
769 | </varlistentry> |
---|
770 | <varlistentry> |
---|
771 | <term>Print map</term> |
---|
772 | <listitem> |
---|
773 | <para>Print map files</para> |
---|
774 | </listitem> |
---|
775 | </varlistentry> |
---|
776 | <varlistentry> |
---|
777 | <term>Protocol</term> |
---|
778 | <listitem> |
---|
779 | <para>Files with protocol information</para> |
---|
780 | </listitem> |
---|
781 | </varlistentry> |
---|
782 | <varlistentry> |
---|
783 | <term>Raw data</term> |
---|
784 | <listitem> |
---|
785 | <para>Raw data files</para> |
---|
786 | </listitem> |
---|
787 | </varlistentry> |
---|
788 | <varlistentry> |
---|
789 | <term>Reporter</term> |
---|
790 | <listitem> |
---|
791 | <para>Files with information about reporters</para> |
---|
792 | </listitem> |
---|
793 | </varlistentry> |
---|
794 | <varlistentry> |
---|
795 | <term>Reporter map</term> |
---|
796 | <listitem> |
---|
797 | <para> |
---|
798 | Files of this type contain information about how the reporters are mapped. |
---|
799 | </para> |
---|
800 | </listitem> |
---|
801 | </varlistentry> |
---|
802 | <varlistentry> |
---|
803 | <term>Spot images</term> |
---|
804 | <listitem> |
---|
805 | <para>A zip-file containing generated spot images in png format.</para> |
---|
806 | </listitem> |
---|
807 | </varlistentry> |
---|
808 | </variablelist> |
---|
809 | </sect1> |
---|
810 | </chapter> |
---|