Changeset 7982 for trunk/doc/historical


Ignore:
Timestamp:
Jun 14, 2021, 10:01:21 AM (20 months ago)
Author:
Nicklas Nordborg
Message:

Merge BASE 3.18.2 to the trunk

Location:
trunk
Files:
8 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/doc/historical/admin/extended-properties.html

    r4889 r7982  
    44    $Id$
    55
    6     Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg
    7     Copyright (C) 2007 Jari Häkkinen
     6    Copyright (C) 2006 Jari Hkkinen, Nicklas Nordborg
     7    Copyright (C) 2007 Jari Hkkinen
    88
    99    This file is part of BASE - BioArray Software Environment.
     
    6060        for ExtendableData</a> </li>
    6161        <li> <a
    62         href="http://base.thep.lu.se/browser/trunk/src/core/net/sf/basedb/core/dtd/extended-properties.dtd">extended-properties.dtd</a> </li>
     62        href="https://base.thep.lu.se/browser/trunk/src/core/net/sf/basedb/core/dtd/extended-properties.dtd">extended-properties.dtd</a> </li>
    6363      </ul>
    6464
     
    110110            The
    111111            <a
    112             href=http://base.thep.lu.se/browser/trunk/config/dist/extended-properties.xml>default
     112            href="https://base.thep.lu.se/browser/trunk/config/dist/extended-properties.xml">default
    113113            extended properties</a> file. The properties described in
    114114            this sample file is required when migration from BASE 1.2
     
    124124            A
    125125            <a
    126             href=http://base.thep.lu.se/browser/trunk/misc/config/minimalistic_extended-properties.xml>minimalistic
     126            href="https://base.thep.lu.se/browser/trunk/misc/config/minimalistic_extended-properties.xml">minimalistic
    127127            setup</a>. This is useful when, at BASE installation time,
    128128            it is not known what reporter data will be stored in the
     
    146146      to follow the straightforward format of
    147147      <a
    148       href=http://base.thep.lu.se/browser/trunk/src/extended-properties.xml>default
     148      href="https://base.thep.lu.se/browser/trunk/src/extended-properties.xml">default
    149149      extended properties</a>. The problem is that some knowledge of
    150150      the underlying database schema is needed.
  • trunk/doc/historical/admin/plugin_configuration/coreplugins.html

    r4889 r7982  
    33  $Id$
    44
    5   Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Martin Svensson
     5  Copyright (C) 2007 Jari Hkkinen, Peter Johansson, Martin Svensson
    66
    77  This file is part of BASE - BioArray Software Environment.
     
    3939      <p>
    4040        This document is mostly superseeded by the <a
    41       href="http://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html">core
     41      href="https://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html">core
    4242        plugins list in the BASE 2 documentation</a>. Some tools are
    4343        still listed here.
     
    5151      <p class="authors">
    5252        <b>Last updated:</b> $Date: 2007-01-09$ <br>
    53         <b>Copyright ©</b> 2007 The respective authors. All rights reserved.
     53        <b>Copyright </b> 2007 The respective authors. All rights reserved.
    5454      </p>
    5555    </div>
  • trunk/doc/historical/development/build.html

    r5656 r7982  
    4141  <div class="warning">
    4242    NOTE! This document is outdated and has been replaced with newer
    43     documentation. See <a href="http://base.thep.lu.se/wiki/BuildingBase">Building BASE from source code</a>
     43    documentation. See <a href="https://base.thep.lu.se/wiki/BuildingBase">Building BASE from source code</a>
    4444  </div>
    4545
     
    9090  </p>
    9191  <pre class="code">
    92 svn checkout http://base.thep.lu.se/svn/trunk/ base
     92svn checkout https://base.thep.lu.se/svn/trunk/ base
    9393</pre>
    9494
     
    9999    For information about how to get other version, including specific releases and bugfix
    100100    branches, read the information on the
    101     <a href="http://base.thep.lu.se/wiki/DownloadPage">BASE download page</a>
    102     or check the <a href="http://base.thep.lu.se/browser">subversion source repository</a>
     101    <a href="https://base.thep.lu.se/wiki/DownloadPage">BASE download page</a>
     102    or check the <a href="https://base.thep.lu.se/browser">subversion source repository</a>
    103103    directly.
    104104  </p>
  • trunk/doc/historical/development/plugins/index.html

    r4889 r7982  
    33  $Id$
    44
    5   Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg
     5  Copyright (C) 2006 Jari Hkkinen, Nicklas Nordborg
    66
    77  This file is part of BASE - BioArray Software Environment.
     
    124124      null,
    125125      "base@thep.lu.se",
    126       "http://base.thep.lu.se"
     126      "https://base.thep.lu.se"
    127127   );
    128128   
  • trunk/doc/historical/test/index.html

    r4889 r7982  
    44    $Id$
    55
    6     Copyright (C) 2006 Jari Häkkinen, Nicklas Nordborg
     6    Copyright (C) 2006 Jari Hkkinen, Nicklas Nordborg
    77
    88    This file is part of BASE - BioArray Software Environment.
     
    7171  target="_new">basedb-devel archive</a>) for discussions about
    7272  BASE 2.0. Please use the <a
    73   href=http://www.edgewall.com/trac/>trac</a> based
     73  href="http://www.edgewall.com/trac/">trac</a> based
    7474  reporting system for bug reports, enhancement ideas, and feature
    7575  requests. More information at <a
    76   href=http://base.thep.lu.se/#Feedback>the feedback section</a> of
    77   the <a href=http://base.thep.lu.se/>BASE trac enviroment</a>.
     76  href="https://base.thep.lu.se/#Feedback">the feedback section</a> of
     77  the <a href="https://base.thep.lu.se/">BASE trac enviroment</a>.
    7878  </p>
    7979
  • trunk/doc/historical/test/merge/index.html

    r4509 r7982  
    7171    <b>See also</b><br>
    7272    <ol>
    73     <li><a href="http://base.thep.lu.se/ticket/215">Ticket #215: Incorrect use of
     73    <li><a href="https://base.thep.lu.se/ticket/215">Ticket #215: Incorrect use of
    7474      DynamicSpotQuery in table view, plot function, filter function, etc.</a>
    7575    </ol>
  • trunk/doc/historical/user/getting_started.html

    r4889 r7982  
    44    $Id$
    55
    6     Copyright (C) 2006 Jari Häkkinen
     6    Copyright (C) 2006 Jari Hkkinen
    77
    88    This file is part of BASE - BioArray Software Environment.
     
    103103            other works out of the box. Some external plug-ins as the
    104104            <a
    105             href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
     105            href="https://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress">RMAExpress
    106106            plug-in for BASE</a> has to be compiled before including
    107107            them into your BASE server.</p>
     
    442442            <p> (Affymetrix only) <b>Install
    443443            <a name=RMAExpressInstall
    444             href=http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress
     444            href="https://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress">RMAExpress
    445445            plug-in for BASE</a></b> <br> This plug-in is required for
    446446            Affymetrix data. The plug-in will create a bioassay set,
     
    650650    BASE. We have not covered how to use the LIMS part of BASE, nor
    651651    annotations, and much more. We are creating documentation, please
    652     browse <a href=http://base.thep.lu.se/>BASE web site</a> for the
     652    browse <a href="https://base.thep.lu.se/">BASE web site</a> for the
    653653    latest available documents. </p>
    654654
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