source: trunk/doc/historical/specifications/migration/index.html

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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 4889 2009-04-06 12:52:39Z nicklas $
4
5  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2006 Johan Enell, Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
7
8  This file is part of BASE - BioArray Software Environment.
9  Available at http://base.thep.lu.se/
10
11  BASE is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License
13  as published by the Free Software Foundation; either version 3
14  of the License, or (at your option) any later version.
15
16  BASE is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19  GNU General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with BASE. If not, see <http://www.gnu.org/licenses/>.
23-->
24<html>
25  <head>
26    <title>BASE - Migration tool specification</title>
27  <link rel=stylesheet type="text/css" href="../../styles.css" />
28</head>
29<body>
30<div class="navigation">
31  <a href="../../index.html">BASE</a>
32  <img src="../../next.gif">
33  Migration tool specifications
34</div>
35
36  <h1>Migration tool specification</h1>
37
38  <div class="abstract">
39    <p>
40    <ol>
41    <li><a href="#Requirements">Requirements</a></li>
42    <li><a href="#QuickStart">QuickStart</a></li>
43
44    <li><a href="#Files">Files</a></li>
45    <li><a href="#Images">Images</a></li>
46    <li><a href="#Plates">Plates</a></li>
47    <li><a href="#Protocols">Protocols</a></li>
48    <li><a href="#Quota">Quota</a></li>
49    <li><a href="#Reporters">Reporters</a></li>
50    <li><a href="#Roles">Roles</a></li>
51    <li><a href="#SampleOrigins">Sample Origins</a></li>
52    <li><a href="base1Tables.html">BASE 1 tables description</a></li>
53    </ol>
54    </p>
55
56    <p class="authors">
57    <b>Contributions by:</b> Gregory<br/>
58    <b>Last updated:</b> $Date: 2009-04-06 12:52:39 +0000 (Mon, 06 Apr 2009) $
59    </p>
60  </div>
61  <br>
62
63
64  <h2>Requirements</h2>
65
66  <p>
67  <ol>
68      <li>Clean and working installation of BASE 2</li>
69    <li>BASE 1 schemeVersion 1.2.20</li>
70    <li>Local or NFS access to BASE 1 file repository</li>
71  </ol>
72  </p>
73
74  <h2>QuickStart</h2>
75
76  <p>
77  First verify that your BASE 2 installation is up and running before attempting
78  migration. Best way to do this is to try to login using the root user
79  through the web interface.
80  <br/>
81  <span class="incode">BASE_HOME</span> - is the root directory of BASE 2 installation
82  package e.g. /home/johndoe/base2-alpha5/
83
84  <ol>
85  <li>Compile migration utility with <br/>
86
87  <span class="incode">
88  &gt; cd BASE_HOME<br/>
89  &gt; ant migrate</span></li>
90  <li>Change migration properties in
91  <b>dist/www/WEB-INF/classes/migrate.properties</b></li>
92  <li>Run migration utility with <br/>
93
94  <span class="incode">
95  &gt; cd BASE_HOME/dist/bin<br/>
96  &gt; ./migrate_from_1.2.sh</span>
97  </li>
98  </ol>
99
100  <div style="border: 5px red solid; padding: 1em;">
101  THERE IS CURRENTLY NO WAY TO CONTINUE A PREVIOUSLY INTERUPTED MIGRATION.
102         YOU HAVE TO RECREATE THE DATABASE AND RERUN THE MIGRATION UTILITY.</div>
103  </p>
104
105
106
107  <a name="Files">
108  <h2>Files</h2>
109  </a>
110  <ul>
111  <li>File names may not have any of the characters
112  &quot;~\\/:;*?&lt;&gt;>|&quot;. These characters will automatically be
113  replaced with and underscore '_' during migration.</li>
114  </ul>
115 
116
117
118
119  <a name="Images">
120  <h2>Images</h2>
121  </a>
122  <ul>
123  <li>Image files from scans that are removed from the uploads shall only be
124  visible to the owner.</li>
125  </ul>
126 
127
128
129
130  <a name="Plates">
131  <h2>Plates</h2>
132  </a>
133  <ul>
134  <li>In BASE 2 mapped plates can have parent plates in arbitrary
135  positions.</li> 
136  <li>Plates with parents using an external file for well mappings are
137  currently not migrated correctly.</li>
138  </ul>
139
140  <a name="Protocols">
141  <h2>Protocols</h2>
142  </a>
143  <ul>
144  <li>Protocols that are linked to files with equal names as currently uploaded files but with different file content are
145  stored in <b>home/USER/protocols</b> directory as ID_FILENAME. Also their creation date is stored in the description.</li>
146  </ul>
147
148
149  <a name="Quota">
150  <h2>Quota</h2>
151  </a>
152  <ul>
153  <li>Each user is assigned one of <a href="../core/defaultdata.html#quota">default quotas</a>.</li>
154  <li>Quota assignment depends on the fileQuota in base 1 and the total usage in BASE 2.</li>
155  </ul>
156
157
158  <a name="Reporters">
159  <h2>Reporters</h2>
160  </a>
161  <ul>
162    <li>Reporters do not get assigned any default ReporterType</li>
163    <li>Start and stop positions are not available in BASE 2</li>
164    <li>Last update date is updated during migration</li>
165  </ul>
166
167  <a name="Roles">
168  <h2>Roles</h2>
169  </a>
170
171  <a name="defaultBaseRoles">
172  <h3>Default BASE Roles</h3>
173  </a>
174 
175  <p>
176    Role assignment is done according to the following protocol:
177  </p>
178 
179  <ol>
180  <li>If <i>Admin privileges &raquo; Superuser</i> is checked that user shall <b><u>only</u></b> 
181    be assigned to the BASE 2 role <b>Administrator</b>.<br/>
182      <ul> 
183      <li>No read restrictions shall be set on users assigned to this role.</li>
184      </ul>
185  </li>
186 
187  <li>If <i>Admin privileges &raquo; Complete read access</i> is checked that user shall be assigned
188    to the BASE 2 role <b>Supervisor</b>.<br/>
189    <ul>
190    <li>No read restrictions shall be set on users assigned to this role.</li>
191    <li>Additional roles may be assigned if the user has more permissions.</li>
192    </ul>
193  </li>
194
195  <li>A user shall be assigned to at most one of the BASE 2 roles <b>Guest</b>, <b>User</b> and
196    <b>Power user</b>:<br/>
197    <ul>
198    <li>Guest: Upload files</li>
199    <li>User: Guest + Add biomaterials, Add hybridizations, Create experiments
200    <li>Power user: User + Add file formats, Add reporters, Add hardware/software,
201      Add annotation types, Add arrays/plates, Add protocols
202    </ul>
203  </li>
204  </ol>
205
206  <p>
207    If the user after this assignment has more permissions that couldn't be matched to a
208    predefined role, the user is assigned to one or more of the migration roles. The migration
209    roles are created by the migration program and have the same name as the BASE 1 permission
210    with the prefix "BASE 1:" added to it.
211  </p>
212
213  <p>
214    C = Create, R = Read, U = Use, W = Write, D = Delete
215  </p>
216
217  <table style="border: 1px solid #000000" cellspacing="0" cellpadding="2" width="100%">
218  <tr style="background: #E0E0E0">
219    <th>BASE 1 permission</th>
220    <th>BASE 2 Permissions</th>
221  </tr>
222 
223  <tr valign="top">
224    <td style="border-top: 1px solid #000000">Administer users</td>
225    <td style="border-top: 1px solid #000000">
226      USER (CRUWD), GROUP (CRUWD), ROLE (CRUWD), <br>
227      QUOTA (CRUWD), QUOTATYPE (RU), DIRECTORY (C)
228    </td>
229  </tr>
230 
231  <tr valign="top">
232    <td style="border-top: 1px solid #000000">Speak in left frame</td>
233    <td style="border-top: 1px solid #000000">
234      Not used by BASE 2.
235    </td>
236  </tr>
237 
238  <tr valign="top">
239    <td style="border-top: 1px solid #000000">Add plug-ins</td>
240    <td style="border-top: 1px solid #000000">PLUGINDEFINITION (C), PLUGINCONFIGURATION (C), PLUGINTYPE (RU)</td>
241  </tr>
242 
243  <tr valign="top">
244    <td style="border-top: 1px solid #000000">Add news</td>
245    <td style="border-top: 1px solid #000000">NEWS (CRUWD)</td>
246  </tr>
247 
248  <tr valign="top">
249    <td style="border-top: 1px solid #000000">Add protocols</td>
250    <td style="border-top: 1px solid #000000">PROTOCOL (CRUWD), PROTOCOLTYPE (RU)</td>
251  </tr>
252 
253  <tr valign="top">
254    <td style="border-top: 1px solid #000000">Add arrays/plates</td>
255    <td style="border-top: 1px solid #000000">
256      PLATEGEOMETRY (RU), PLATETYPE (C), PLATE (C), PLATEMAPPING (RU),<br>
257      ARRAYDESIGN (C), ARRAYBATCH (C), ARRAYSLIDE (C), PROTOCOLTYPE (RU)
258    </td>
259  </tr>
260 
261  <tr valign="top">
262    <td style="border-top: 1px solid #000000">Add annotation types</td>
263    <td style="border-top: 1px solid #000000">
264      ANNOTATIONTYPE (C), ANNOTATIONTYPECATEGORY (C)
265    </td>
266  </tr>
267
268  <tr valign="top">
269    <td style="border-top: 1px solid #000000">Add hardware/software</td>
270    <td style="border-top: 1px solid #000000">
271      HARDWARE (C), HARDWARETYPE (RU), SOFTWARE (C), SOFTWARETYPE (RU)
272    </td>
273  </tr>
274
275  <tr valign="top">
276    <td style="border-top: 1px solid #000000">Add reporters</td>
277    <td style="border-top: 1px solid #000000">
278      REPORTER (CRUWD), REPORERTYPE (CRUWD), REPORTERLIST (C)
279    </td>
280  </tr>
281
282  <tr valign="top">
283    <td style="border-top: 1px solid #000000">Add file formats</td>
284    <td style="border-top: 1px solid #000000">
285      PLUGINCONFIGURATION (C)
286    </td>
287  </tr>
288
289  <tr valign="top">
290    <td style="border-top: 1px solid #000000">Read more user info</td>
291    <td style="border-top: 1px solid #000000">
292      -
293    </td>
294  </tr>
295
296  <tr valign="top">
297    <td style="border-top: 1px solid #000000">Read plugins (if missing)</td>
298    <td style="border-top: 1px solid #000000">
299      PLUGINDEFINITION (DENIED), PLUGINCONFIGURATION (DENIED)
300    </td>
301  </tr>
302
303  <tr valign="top">
304    <td style="border-top: 1px solid #000000">Create MAGE-ML file</td>
305    <td style="border-top: 1px solid #000000">
306      -
307    </td>
308  </tr>
309
310  <tr valign="top">
311    <td style="border-top: 1px solid #000000">Share with world</td>
312    <td style="border-top: 1px solid #000000">
313      SHARE_TO_EVERYONE
314    </td>
315  </tr>
316
317  <tr valign="top">
318    <td style="border-top: 1px solid #000000">Add biomaterials</td>
319    <td style="border-top: 1px solid #000000">
320      BIOSOURCE (C), SAMPLE (C), EXTRACT (C), LABELEDEXTRACT (C), LABEL (C)
321    </td>
322  </tr>
323
324  <tr valign="top">
325    <td style="border-top: 1px solid #000000">Add hybridization</td>
326    <td style="border-top: 1px solid #000000">
327      HYBRIDIZATION (C), SCAN (C), RAWBIOASSAY (C)
328    </td>
329  </tr>
330
331  <tr valign="top">
332    <td style="border-top: 1px solid #000000">Create experiments</td>
333    <td style="border-top: 1px solid #000000">
334      EXPERIMENT (C)
335    </td>
336  </tr>
337 
338  <tr valign="top">
339    <td style="border-top: 1px solid #000000">Edit experiments</td>
340    <td style="border-top: 1px solid #000000">
341      -
342    </td>
343  </tr>
344
345  <tr valign="top">
346    <td style="border-top: 1px solid #000000">Upload files</td>
347    <td style="border-top: 1px solid #000000">
348      FILE (C), DIRECTORY (C)
349    </td>
350  </tr>
351
352  <tr valign="top">
353    <td style="border-top: 1px solid #000000">Read arrays/plates (if missing)</td>
354    <td style="border-top: 1px solid #000000">
355      PLATEGEOMETRY (DENIED), PLATETYPE (DENIED), PLATE (DENIED), <br>
356      PLATEMAPPING (DENIED), ARRAYDESIGN (DENIED),<br>
357      ARRAYBATCH (DENIED), ARRAYSLIDE (DENIED)
358    </td>
359  </tr>
360 
361  <tr valign="top">
362    <td style="border-top: 1px solid #000000">Read user info (if missing)</td>
363    <td style="border-top: 1px solid #000000">
364      USER (DENIED)
365    </td>
366  </tr>
367 
368  <tr valign="top">
369    <td style="border-top: 1px solid #000000">Read biomaterials (if missing)</td>
370    <td style="border-top: 1px solid #000000">
371      BIOSOURCE (DENIED), SAMPLE (DENIED), EXTRACT (DENIED),<br>
372      LABELEDEXTRACT (DENIED), LABEL (DENIED)
373    </td>
374  </tr>
375 
376  <tr valign="top">
377    <td style="border-top: 1px solid #000000">Read hybridizations (if missing)</td>
378    <td style="border-top: 1px solid #000000">
379      HYBRIDIZATION (DENIED), SCAN (DENIED), RAWBIOASSAY (DENIED)
380    </td>
381  </tr>
382 
383  <tr valign="top">
384    <td style="border-top: 1px solid #000000">Read experiments (if missing)</td>
385    <td style="border-top: 1px solid #000000">
386      EXPERIMENT (DENIED)
387    </td>
388  </tr>
389 
390  <tr valign="top">
391    <td style="border-top: 1px solid #000000">Read reporters</td>
392    <td style="border-top: 1px solid #000000">
393      REPORTER (RU), REPORTERTYPE (RU)
394    </td>
395  </tr>
396  </table>
397
398  <a name="SampleOrigins">
399  <h2>Sample Origins</h2>
400  </a>
401  <ol>
402  <li>Sample origins are not available in BASE 2, though they are added to the description of each sample as<br/>
403  eg. Human -> Cell Line -> ...
404  </li>
405  </ol>
406
407</body>
408</html>
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