source: trunk/doc/historical/specifications/migration/index.html @ 4394

Last change on this file since 4394 was 3679, checked in by Jari Häkkinen, 16 years ago

Changing the pesky "a (ä) character to a.
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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 3679 2007-08-17 07:18:29Z jari $
4
5  Copyright (C) 2005 Nicklas Nordborg, Gregory Vincic
6  Copyright (C) 2006 Johan Enell, Jari Hakkinen, 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 2
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 this program; if not, write to the Free Software
23  Foundation, Inc., 59 Temple Place - Suite 330,
24  Boston, MA  02111-1307, USA.
25-->
26<html>
27  <head>
28    <title>BASE - Migration tool specification</title>
29  <link rel=stylesheet type="text/css" href="../../styles.css" />
30</head>
31<body>
32<div class="navigation">
33  <a href="../../index.html">BASE</a>
34  <img src="../../next.gif">
35  Migration tool specifications
36</div>
37
38  <h1>Migration tool specification</h1>
39
40  <div class="abstract">
41    <p>
42    <ol>
43    <li><a href="#Requirements">Requirements</a></li>
44    <li><a href="#QuickStart">QuickStart</a></li>
45
46    <li><a href="#Files">Files</a></li>
47    <li><a href="#Images">Images</a></li>
48    <li><a href="#Plates">Plates</a></li>
49    <li><a href="#Protocols">Protocols</a></li>
50    <li><a href="#Quota">Quota</a></li>
51    <li><a href="#Reporters">Reporters</a></li>
52    <li><a href="#Roles">Roles</a></li>
53    <li><a href="#SampleOrigins">Sample Origins</a></li>
54    <li><a href="base1Tables.html">BASE 1 tables description</a></li>
55    </ol>
56    </p>
57
58    <p class="authors">
59    <b>Contributions by:</b> Gregory<br/>
60    <b>Last updated:</b> $Date: 2007-08-17 07:18:29 +0000 (Fri, 17 Aug 2007) $
61    </p>
62  </div>
63  <br>
64
65
66  <h2>Requirements</h2>
67
68  <p>
69  <ol>
70      <li>Clean and working installation of BASE 2</li>
71    <li>BASE 1 schemeVersion 1.2.20</li>
72    <li>Local or NFS access to BASE 1 file repository</li>
73  </ol>
74  </p>
75
76  <h2>QuickStart</h2>
77
78  <p>
79  First verify that your BASE 2 installation is up and running before attempting
80  migration. Best way to do this is to try to login using the root user
81  through the web interface.
82  <br/>
83  <span class="incode">BASE_HOME</span> - is the root directory of BASE 2 installation
84  package e.g. /home/johndoe/base2-alpha5/
85
86  <ol>
87  <li>Compile migration utility with <br/>
88
89  <span class="incode">
90  &gt; cd BASE_HOME<br/>
91  &gt; ant migrate</span></li>
92  <li>Change migration properties in
93  <b>dist/www/WEB-INF/classes/migrate.properties</b></li>
94  <li>Run migration utility with <br/>
95
96  <span class="incode">
97  &gt; cd BASE_HOME/dist/bin<br/>
98  &gt; ./migrate_from_1.2.sh</span>
99  </li>
100  </ol>
101
102  <div style="border: 5px red solid; padding: 1em;">
103  THERE IS CURRENTLY NO WAY TO CONTINUE A PREVIOUSLY INTERUPTED MIGRATION.
104         YOU HAVE TO RECREATE THE DATABASE AND RERUN THE MIGRATION UTILITY.</div>
105  </p>
106
107
108
109  <a name="Files">
110  <h2>Files</h2>
111  </a>
112  <ul>
113  <li>File names may not have any of the characters
114  &quot;~\\/:;*?&lt;&gt;>|&quot;. These characters will automatically be
115  replaced with and underscore '_' during migration.</li>
116  </ul>
117 
118
119
120
121  <a name="Images">
122  <h2>Images</h2>
123  </a>
124  <ul>
125  <li>Image files from scans that are removed from the uploads shall only be
126  visible to the owner.</li>
127  </ul>
128 
129
130
131
132  <a name="Plates">
133  <h2>Plates</h2>
134  </a>
135  <ul>
136  <li>In BASE 2 mapped plates can have parent plates in arbitrary
137  positions.</li> 
138  <li>Plates with parents using an external file for well mappings are
139  currently not migrated correctly.</li>
140  </ul>
141
142  <a name="Protocols">
143  <h2>Protocols</h2>
144  </a>
145  <ul>
146  <li>Protocols that are linked to files with equal names as currently uploaded files but with different file content are
147  stored in <b>home/USER/protocols</b> directory as ID_FILENAME. Also their creation date is stored in the description.</li>
148  </ul>
149
150
151  <a name="Quota">
152  <h2>Quota</h2>
153  </a>
154  <ul>
155  <li>Each user is assigned one of <a href="../core/defaultdata.html#quota">default quotas</a>.</li>
156  <li>Quota assignment depends on the fileQuota in base 1 and the total usage in BASE 2.</li>
157  </ul>
158
159
160  <a name="Reporters">
161  <h2>Reporters</h2>
162  </a>
163  <ul>
164    <li>Reporters do not get assigned any default ReporterType</li>
165    <li>Start and stop positions are not available in BASE 2</li>
166    <li>Last update date is updated during migration</li>
167  </ul>
168
169  <a name="Roles">
170  <h2>Roles</h2>
171  </a>
172
173  <a name="defaultBaseRoles">
174  <h3>Default BASE Roles</h3>
175  </a>
176 
177  <p>
178    Role assignment is done according to the following protocol:
179  </p>
180 
181  <ol>
182  <li>If <i>Admin privileges &raquo; Superuser</i> is checked that user shall <b><u>only</u></b> 
183    be assigned to the BASE 2 role <b>Administrator</b>.<br/>
184      <ul> 
185      <li>No read restrictions shall be set on users assigned to this role.</li>
186      </ul>
187  </li>
188 
189  <li>If <i>Admin privileges &raquo; Complete read access</i> is checked that user shall be assigned
190    to the BASE 2 role <b>Supervisor</b>.<br/>
191    <ul>
192    <li>No read restrictions shall be set on users assigned to this role.</li>
193    <li>Additional roles may be assigned if the user has more permissions.</li>
194    </ul>
195  </li>
196
197  <li>A user shall be assigned to at most one of the BASE 2 roles <b>Guest</b>, <b>User</b> and
198    <b>Power user</b>:<br/>
199    <ul>
200    <li>Guest: Upload files</li>
201    <li>User: Guest + Add biomaterials, Add hybridizations, Create experiments
202    <li>Power user: User + Add file formats, Add reporters, Add hardware/software,
203      Add annotation types, Add arrays/plates, Add protocols
204    </ul>
205  </li>
206  </ol>
207
208  <p>
209    If the user after this assignment has more permissions that couldn't be matched to a
210    predefined role, the user is assigned to one or more of the migration roles. The migration
211    roles are created by the migration program and have the same name as the BASE 1 permission
212    with the prefix "BASE 1:" added to it.
213  </p>
214
215  <p>
216    C = Create, R = Read, U = Use, W = Write, D = Delete
217  </p>
218
219  <table style="border: 1px solid #000000" cellspacing="0" cellpadding="2" width="100%">
220  <tr style="background: #E0E0E0">
221    <th>BASE 1 permission</th>
222    <th>BASE 2 Permissions</th>
223  </tr>
224 
225  <tr valign="top">
226    <td style="border-top: 1px solid #000000">Administer users</td>
227    <td style="border-top: 1px solid #000000">
228      USER (CRUWD), GROUP (CRUWD), ROLE (CRUWD), <br>
229      QUOTA (CRUWD), QUOTATYPE (RU), DIRECTORY (C)
230    </td>
231  </tr>
232 
233  <tr valign="top">
234    <td style="border-top: 1px solid #000000">Speak in left frame</td>
235    <td style="border-top: 1px solid #000000">
236      Not used by BASE 2.
237    </td>
238  </tr>
239 
240  <tr valign="top">
241    <td style="border-top: 1px solid #000000">Add plug-ins</td>
242    <td style="border-top: 1px solid #000000">PLUGINDEFINITION (C), PLUGINCONFIGURATION (C), PLUGINTYPE (RU)</td>
243  </tr>
244 
245  <tr valign="top">
246    <td style="border-top: 1px solid #000000">Add news</td>
247    <td style="border-top: 1px solid #000000">NEWS (CRUWD)</td>
248  </tr>
249 
250  <tr valign="top">
251    <td style="border-top: 1px solid #000000">Add protocols</td>
252    <td style="border-top: 1px solid #000000">PROTOCOL (CRUWD), PROTOCOLTYPE (RU)</td>
253  </tr>
254 
255  <tr valign="top">
256    <td style="border-top: 1px solid #000000">Add arrays/plates</td>
257    <td style="border-top: 1px solid #000000">
258      PLATEGEOMETRY (RU), PLATETYPE (C), PLATE (C), PLATEMAPPING (RU),<br>
259      ARRAYDESIGN (C), ARRAYBATCH (C), ARRAYSLIDE (C), PROTOCOLTYPE (RU)
260    </td>
261  </tr>
262 
263  <tr valign="top">
264    <td style="border-top: 1px solid #000000">Add annotation types</td>
265    <td style="border-top: 1px solid #000000">
266      ANNOTATIONTYPE (C), ANNOTATIONTYPECATEGORY (C)
267    </td>
268  </tr>
269
270  <tr valign="top">
271    <td style="border-top: 1px solid #000000">Add hardware/software</td>
272    <td style="border-top: 1px solid #000000">
273      HARDWARE (C), HARDWARETYPE (RU), SOFTWARE (C), SOFTWARETYPE (RU)
274    </td>
275  </tr>
276
277  <tr valign="top">
278    <td style="border-top: 1px solid #000000">Add reporters</td>
279    <td style="border-top: 1px solid #000000">
280      REPORTER (CRUWD), REPORERTYPE (CRUWD), REPORTERLIST (C)
281    </td>
282  </tr>
283
284  <tr valign="top">
285    <td style="border-top: 1px solid #000000">Add file formats</td>
286    <td style="border-top: 1px solid #000000">
287      PLUGINCONFIGURATION (C)
288    </td>
289  </tr>
290
291  <tr valign="top">
292    <td style="border-top: 1px solid #000000">Read more user info</td>
293    <td style="border-top: 1px solid #000000">
294      -
295    </td>
296  </tr>
297
298  <tr valign="top">
299    <td style="border-top: 1px solid #000000">Read plugins (if missing)</td>
300    <td style="border-top: 1px solid #000000">
301      PLUGINDEFINITION (DENIED), PLUGINCONFIGURATION (DENIED)
302    </td>
303  </tr>
304
305  <tr valign="top">
306    <td style="border-top: 1px solid #000000">Create MAGE-ML file</td>
307    <td style="border-top: 1px solid #000000">
308      -
309    </td>
310  </tr>
311
312  <tr valign="top">
313    <td style="border-top: 1px solid #000000">Share with world</td>
314    <td style="border-top: 1px solid #000000">
315      SHARE_TO_EVERYONE
316    </td>
317  </tr>
318
319  <tr valign="top">
320    <td style="border-top: 1px solid #000000">Add biomaterials</td>
321    <td style="border-top: 1px solid #000000">
322      BIOSOURCE (C), SAMPLE (C), EXTRACT (C), LABELEDEXTRACT (C), LABEL (C)
323    </td>
324  </tr>
325
326  <tr valign="top">
327    <td style="border-top: 1px solid #000000">Add hybridization</td>
328    <td style="border-top: 1px solid #000000">
329      HYBRIDIZATION (C), SCAN (C), RAWBIOASSAY (C)
330    </td>
331  </tr>
332
333  <tr valign="top">
334    <td style="border-top: 1px solid #000000">Create experiments</td>
335    <td style="border-top: 1px solid #000000">
336      EXPERIMENT (C)
337    </td>
338  </tr>
339 
340  <tr valign="top">
341    <td style="border-top: 1px solid #000000">Edit experiments</td>
342    <td style="border-top: 1px solid #000000">
343      -
344    </td>
345  </tr>
346
347  <tr valign="top">
348    <td style="border-top: 1px solid #000000">Upload files</td>
349    <td style="border-top: 1px solid #000000">
350      FILE (C), DIRECTORY (C)
351    </td>
352  </tr>
353
354  <tr valign="top">
355    <td style="border-top: 1px solid #000000">Read arrays/plates (if missing)</td>
356    <td style="border-top: 1px solid #000000">
357      PLATEGEOMETRY (DENIED), PLATETYPE (DENIED), PLATE (DENIED), <br>
358      PLATEMAPPING (DENIED), ARRAYDESIGN (DENIED),<br>
359      ARRAYBATCH (DENIED), ARRAYSLIDE (DENIED)
360    </td>
361  </tr>
362 
363  <tr valign="top">
364    <td style="border-top: 1px solid #000000">Read user info (if missing)</td>
365    <td style="border-top: 1px solid #000000">
366      USER (DENIED)
367    </td>
368  </tr>
369 
370  <tr valign="top">
371    <td style="border-top: 1px solid #000000">Read biomaterials (if missing)</td>
372    <td style="border-top: 1px solid #000000">
373      BIOSOURCE (DENIED), SAMPLE (DENIED), EXTRACT (DENIED),<br>
374      LABELEDEXTRACT (DENIED), LABEL (DENIED)
375    </td>
376  </tr>
377 
378  <tr valign="top">
379    <td style="border-top: 1px solid #000000">Read hybridizations (if missing)</td>
380    <td style="border-top: 1px solid #000000">
381      HYBRIDIZATION (DENIED), SCAN (DENIED), RAWBIOASSAY (DENIED)
382    </td>
383  </tr>
384 
385  <tr valign="top">
386    <td style="border-top: 1px solid #000000">Read experiments (if missing)</td>
387    <td style="border-top: 1px solid #000000">
388      EXPERIMENT (DENIED)
389    </td>
390  </tr>
391 
392  <tr valign="top">
393    <td style="border-top: 1px solid #000000">Read reporters</td>
394    <td style="border-top: 1px solid #000000">
395      REPORTER (RU), REPORTERTYPE (RU)
396    </td>
397  </tr>
398  </table>
399
400  <a name="SampleOrigins">
401  <h2>Sample Origins</h2>
402  </a>
403  <ol>
404  <li>Sample origins are not available in BASE 2, though they are added to the description of each sample as<br/>
405  eg. Human -> Cell Line -> ...
406  </li>
407  </ol>
408
409</body>
410</html>
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