| 1 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> |
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| 2 | <!-- |
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| 3 | $Id: importexport.html 4509 2008-09-11 20:01:44Z jari $ |
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| 4 | |
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| 5 | Copyright (C) 2005 Jari Hakkinen, Nicklas Nordborg |
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| 6 | Copyright (C) 2006 Jari Hakkinen |
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| 7 | |
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| 8 | This file is part of BASE - BioArray Software Environment. |
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| 9 | Available at http://base.thep.lu.se/ |
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| 10 | |
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| 11 | BASE is free software; you can redistribute it and/or |
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| 12 | modify it under the terms of the GNU General Public License |
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| 13 | as published by the Free Software Foundation; either version 3 |
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| 14 | of the License, or (at your option) any later version. |
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| 15 | |
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| 16 | BASE is distributed in the hope that it will be useful, |
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| 17 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 18 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 19 | GNU General Public License for more details. |
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| 20 | |
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| 21 | You should have received a copy of the GNU General Public License |
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| 22 | along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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| 23 | --> |
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| 24 | <html> |
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| 25 | <head> |
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| 26 | <title>BASE - Core specification - Data import and export</title> |
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| 27 | <link rel=stylesheet type="text/css" href="../../styles.css"> |
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| 28 | </head> |
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| 29 | <body> |
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| 30 | |
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| 31 | <div class="navigation"> |
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| 32 | <a href="../../index.html">BASE</a> |
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| 33 | <img src="../../next.gif"> |
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| 34 | <a href="index.html">Core specification</a> |
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| 35 | <img src="../../next.gif"> |
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| 36 | Data import and export |
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| 37 | </div> |
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| 38 | |
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| 39 | <h1>Data import and export</h1> |
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| 40 | |
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| 41 | <div class="abstract"> |
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| 42 | <p> |
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| 43 | This document covers details for data import and export and how it can be |
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| 44 | extended to support more file formats by the use of plugins. |
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| 45 | </p> |
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| 46 | |
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| 47 | <b>Contents</b><br> |
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| 48 | <ol> |
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| 49 | <li><a href="#import">Import</a> |
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| 50 | <li><a href="#export">Export</a> |
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| 51 | </ol> |
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| 52 | |
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| 53 | <p class="authors"> |
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| 54 | <b>Last updated:</b> $Date: 2008-09-11 20:01:44 +0000 (Thu, 11 Sep 2008) $ |
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| 55 | </p> |
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| 56 | </div> |
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| 57 | |
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| 58 | <a name="import"> |
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| 59 | <h2>1. Import</h2> |
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| 60 | </a> |
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| 61 | |
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| 62 | <ol> |
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| 63 | <li>The parsing of files for importing data is handled entirely by plugins. |
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| 64 | |
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| 65 | <li>The core will include a plugin for parsing tab-separated files. |
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| 66 | |
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| 67 | <li>Insertion of parsed data into the database can be done |
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| 68 | in two ways: |
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| 69 | <ol> |
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| 70 | <li>The plugin uses the core API to insert the data |
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| 71 | <li>The plugin returns the information to the core which inserts the |
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| 72 | data |
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| 73 | </ol> |
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| 74 | <div class="note">[NOTE] |
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| 75 | The first method is the most flexible and allows a plugin to parse files |
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| 76 | with more than one type of items. The second method requires that the core |
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| 77 | knows what types of items are in the file. An exemple of the first type is |
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| 78 | a plugin that parses an XML file containing structured biomaterial data, |
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| 79 | ie. samples, extracts and labeled extracts. All file formats that are used |
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| 80 | in BASE 1.x can be implemented as a type 2 plugin. |
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| 81 | </div> |
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| 82 | |
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| 83 | <li>A plugin should be able to check if a file is parsable by that plugin. |
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| 84 | For example, a plugin that expects XML data should not be used on |
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| 85 | tab-separated data. The plugin may also check headers, the number of |
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| 86 | columns, and other information appearing in the file. |
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| 87 | |
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| 88 | <li> |
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| 89 | |
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| 90 | |
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| 91 | </ol> |
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| 92 | |
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| 93 | |
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| 94 | <a name="export"> |
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| 95 | <h2>2. Export</h2> |
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| 96 | </a> |
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| 97 | |
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| 98 | <ol> |
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| 99 | <li>Exporting data is handled entirely by plugins. |
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| 100 | |
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| 101 | <li>A plugin may need input parameters from the user to |
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| 102 | select options for the export. |
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| 103 | |
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| 104 | <li>The type and acceptable values of the input parameters must |
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| 105 | be defined in a standardised way to allow various client applications |
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| 106 | to display a form asking for values. |
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| 107 | |
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| 108 | <li>The plugin should use the core API to read the data. |
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| 109 | |
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| 110 | <li> |
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| 111 | |
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| 112 | </ol> |
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| 113 | |
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| 114 | |
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| 115 | </body> |
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| 116 | </html> |
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| 117 | |
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