Changeset 7978


Ignore:
Timestamp:
Jun 11, 2021, 12:51:05 PM (6 months ago)
Author:
Nicklas Nordborg
Message:

References #2257: base.thep.lu.se is moving to https

Updated lots of links in the documentation.

Location:
branches/3.18-stable
Files:
32 edited

Legend:

Unmodified
Added
Removed
  • branches/3.18-stable/doc/historical/admin/extended-properties.html

    r4889 r7978  
    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.
  • branches/3.18-stable/doc/historical/admin/plugin_configuration/coreplugins.html

    r4889 r7978  
    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>
  • branches/3.18-stable/doc/historical/development/build.html

    r5656 r7978  
    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>
  • branches/3.18-stable/doc/historical/development/plugins/index.html

    r4889 r7978  
    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   
  • branches/3.18-stable/doc/historical/test/index.html

    r4889 r7978  
    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
  • branches/3.18-stable/doc/historical/test/merge/index.html

    r4509 r7978  
    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>
  • branches/3.18-stable/doc/historical/user/getting_started.html

    r4889 r7978  
    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
  • branches/3.18-stable/doc/src/docbook/admin/installation.xml

    r7916 r7978  
    157157                  This option is for advanced users only and is not
    158158                  covered here. Please refer to
    159                   <ulink url="http://base.thep.lu.se/wiki/BuildingBase" /> for information on
     159                  <ulink url="https://base.thep.lu.se/wiki/BuildingBase" /> for information on
    160160                  this download option.
    161161                </para>
     
    420420          <para>
    421421            <ulink
    422             url="http://base.thep.lu.se/wiki/DownloadPage">Download
     422            url="https://base.thep.lu.se/wiki/DownloadPage">Download
    423423            BASE</ulink> and unpack the downloaded file,
    424424            i.e. <command>tar zxpf base-...tar.gz</command>. If you
     
    426426            a checkout of the source from the subversion repository
    427427            (subversion checkout instructions at
    428             <ulink url="http://base.thep.lu.se/wiki/DownloadPage">BASE
     428            <ulink url="https://base.thep.lu.se/wiki/DownloadPage">BASE
    429429            trac site</ulink>).
    430430          </para>
     
    451451              is available in the
    452452              <ulink
    453               url="http://base.thep.lu.se/wiki/BuildingBase">building
     453              url="https://base.thep.lu.se/wiki/BuildingBase">building
    454454              BASE document</ulink>. When you return back after
    455455              compiling in the subversion tree you can follow the
     
    530530            There is an
    531531            administrator <ulink
    532             url="http://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document
     532            url="https://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document
    533533            discussing extended properties</ulink> available. If you
    534534            plan to perform a migration of a BASE version 1.2 database you
     
    906906                downloads at
    907907                <ulink
    908                 url="http://base.thep.lu.se/wiki/DownloadPage">http://base.thep.lu.se/wiki/DownloadPage</ulink>
     908                url="https://base.thep.lu.se/wiki/DownloadPage">https://base.thep.lu.se/wiki/DownloadPage</ulink>
    909909              </para>
    910910            </listitem>
     
    13631363                    BASE version on the BASE web site,
    13641364                    <ulink
    1365                       url="http://base.thep.lu.se/chrome/site/doc/html/index.html">
    1366                       http://base.thep.lu.se/chrome/site/doc/html/index.html</ulink>.
     1365                      url="https://base.thep.lu.se/chrome/site/doc/html/index.html">
     1366                      https://base.thep.lu.se/chrome/site/doc/html/index.html</ulink>.
    13671367                   
    13681368                    If you want the documentation for a specific version you will
     
    13901390                    perhaps other feedback that concerns the program. As default
    13911391                    this is set to the feedback section on BASE web site,
    1392                     <ulink url="http://base.thep.lu.se/#Feedback">http://base.thep.lu.se/#Feedback</ulink>.
     1392                    <ulink url="https://base.thep.lu.se/#Feedback">https://base.thep.lu.se/#Feedback</ulink>.
    13931393                    Note that users must login in order to submit information.
    13941394                  </para>
  • branches/3.18-stable/doc/src/docbook/appendix/base.config.xml

    r7598 r7978  
    829829      If you want to setup your own test environment with a https server that only
    830830      accepts clients with a trusted certificate you can find some information about
    831       this on our wiki: <ulink url="http://base.thep.lu.se/wiki/HttpsFiles"
    832       >http://base.thep.lu.se/wiki/HttpsFiles</ulink>
     831      this on our wiki: <ulink url="https://base.thep.lu.se/wiki/HttpsFiles"
     832      >https://base.thep.lu.se/wiki/HttpsFiles</ulink>
    833833    </para>
    834834   
  • branches/3.18-stable/doc/src/docbook/appendix/coreplugins.xml

    r7640 r7978  
    4242  <para>
    4343    Contributed plug-ins are available at <ulink
    44     url="http://baseplugins.thep.lu.se" >http://baseplugins.thep.lu.se
     44    url="https://baseplugins.thep.lu.se" >https://baseplugins.thep.lu.se
    4545    </ulink>. These plug-ins are either developed outside the core team
    4646    or require external non-Java compilers and tools. These packages
  • branches/3.18-stable/doc/src/docbook/appendix/incompatible.xml

    r7681 r7978  
    201201      other clients that use a different client id are affected and may stop to work
    202202      until they have been updated to use the new API. For more information see
    203       <ulink url="http://base.thep.lu.se/ticket/2011">ticket 2011</ulink>.
     203      <ulink url="https://base.thep.lu.se/ticket/2011">ticket 2011</ulink>.
    204204    </para>
    205205   
     
    345345        event handlers and script sections since this is a possible entry
    346346        point for cross-site scripting attacks (see <ulink
    347           url="http://base.thep.lu.se/ticket/1712">ticket 1712</ulink>).
     347          url="https://base.thep.lu.se/ticket/1712">ticket 1712</ulink>).
    348348        Extension developers are encouraged to make the same changes in
    349349        their applications.
     
    469469      for the best user experience. The changes are too numerous so we can't
    470470      list them here. Please use the developers mailing list if specific
    471       information is needed or see <ulink url="http://base.thep.lu.se/ticket/1655">ticket
     471      information is needed or see <ulink url="https://base.thep.lu.se/ticket/1655">ticket
    472472      1655</ulink> for some screenshots and other information.
    473473    </para>
     
    484484      may cause problems for code that is expecting all annotations to be
    485485      available. See <classname docapi="net.sf.basedb.core">ReporterCloneTemplate</classname>
    486       and <ulink url="http://base.thep.lu.se/ticket/1616">ticket 1616</ulink>
     486      and <ulink url="https://base.thep.lu.se/ticket/1616">ticket 1616</ulink>
    487487      for more information.
    488488    </para>
     
    497497      this situation. Particulary, infinite loops must be avoided when traversing the "parent"
    498498      tree of an item (but this should already be in place since it can already happen due to
    499       mistakes when creating items). See <ulink url="http://base.thep.lu.se/ticket/1605">ticket 1605</ulink>
     499      mistakes when creating items). See <ulink url="https://base.thep.lu.se/ticket/1605">ticket 1605</ulink>
    500500      for more information.
    501501    </para>
     
    520520    <para>
    521521      The list of changes made in the various BASE 2.x releases can be found
    522       in the <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/appendix/appendix.incompatible.html"
     522      in the <ulink url="https://base.thep.lu.se/chrome/site/2.17/html/appendix/appendix.incompatible.html"
    523523      >BASE 2.17 documentation</ulink>.
    524524    </para>
  • branches/3.18-stable/doc/src/docbook/appendix/update_warnings.xml

    r7916 r7978  
    571571      We only support updating to BASE 3 from BASE 2.17. If you have an older BASE
    572572      version and wish to update to BASE 3, you first have to upgrade to BASE 2.17.
    573       BASE 2.17 can be downloaded from the <ulink url="http://base.thep.lu.se/wiki/DownloadPage">BASE
     573      BASE 2.17 can be downloaded from the <ulink url="https://base.thep.lu.se/wiki/DownloadPage">BASE
    574574      download page</ulink>. Documentation for BASE 2.17 is available as part of the
    575       download and at <ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html"
    576       >http://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>.
     575      download and at <ulink url="https://base.thep.lu.se/chrome/site/2.17/html/index.html"
     576      >https://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>.
    577577    </para>
    578578
  • branches/3.18-stable/doc/src/docbook/appendix/web.xml.xml

    r7609 r7978  
    6464        of a POST request instead. This functionality can disabled by
    6565        setting this value to 0. For more information see
    66         <ulink url="http://base.thep.lu.se/ticket/1032">http://base.thep.lu.se/ticket/1032</ulink>.
     66        <ulink url="https://base.thep.lu.se/ticket/1032">https://base.thep.lu.se/ticket/1032</ulink>.
    6767        </para>
    6868      </listitem>
  • branches/3.18-stable/doc/src/docbook/developer/base_api.xml

    r7640 r7978  
    24992499        This documentation is only available in the old format which may not be up-to-date with
    25002500        the current implementation.
    2501         See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html"
    2502           >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html</ulink>
     2501        See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html"
     2502          >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/authentication.html</ulink>
    25032503      </para>
    25042504    </sect2>   
     
    25092509        This documentation is only available in the old format which may not be up-to-date with
    25102510        the current implementation.
    2511         See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html"
    2512           >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html</ulink>
     2511        See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html"
     2512          >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/accesspermissions.html</ulink>
    25132513      </para>
    25142514    </sect2>
     
    25312531        This documentation is only available in the old format which may not be up-to-date with
    25322532        the current implementation.
    2533         See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html"
    2534           >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html</ulink>
     2533        See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html"
     2534          >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/itemhandling.html</ulink>
    25352535      </para>
    25362536    </sect2>   
     
    25402540        This documentation is only available in the old format which may not be up-to-date with
    25412541        the current implementation.
    2542         See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html"
    2543           >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html</ulink>
     2542        See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html"
     2543          >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/batchprocessing.html</ulink>
    25442544      </para>
    25452545    </sect2>   
     
    25562556        This documentation is only available in the old format which may not be up-to-date with
    25572557        the current implementation.
    2558         See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html"
    2559           >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html</ulink>
     2558        See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html"
     2559          >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/core/plugins.html</ulink>
    25602560      </para>
    25612561    </sect2>   
     
    31613161      This documentation is only available in the old format which may not be up-to-date with
    31623162      the current implementation.
    3163       See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html"
    3164         >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html</ulink>
     3163      See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html"
     3164        >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/query/index.html</ulink>
    31653165    </para>
    31663166   
     
    31733173      This documentation is only available in the old format which may not be up-to-date with
    31743174      the current implementation.
    3175       See <ulink url="http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html"
    3176         >http://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html</ulink>
     3175      See <ulink url="https://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html"
     3176        >https://base.thep.lu.se/chrome/site/doc/historical/development/overview/dynamic/index.html</ulink>
    31773177    </para>
    31783178  </sect1>
  • branches/3.18-stable/doc/src/docbook/developer/core_ref.xml

    r6912 r7978  
    3131    <title>Publishing a new release</title>
    3232    <para>
    33       This documentation is available on the <ulink url="http://base.thep.lu.se/wiki/ReleaseProcedure">BASE wiki</ulink>.
     33      This documentation is available on the <ulink url="https://base.thep.lu.se/wiki/ReleaseProcedure">BASE wiki</ulink>.
    3434    </para>
    3535  </sect1>
     
    3838    <title>Subversion / building BASE</title>
    3939    <para>
    40       This documentation is available on the <ulink url="http://base.thep.lu.se/wiki/BuildingBase">BASE wiki</ulink>.
     40      This documentation is available on the <ulink url="https://base.thep.lu.se/wiki/BuildingBase">BASE wiki</ulink>.
    4141    </para>
    4242  </sect1>
     
    586586
    587587   This file is part of BASE - BioArray Software Environment.
    588    Available at http://base.thep.lu.se/
     588   Available at https://base.thep.lu.se/
    589589
    590590   BASE is free software; you can redistribute it and/or
     
    30693069
    30703070  This file is part of BASE - BioArray Software Environment.
    3071   Available at http://base.thep.lu.se/
     3071  Available at https://base.thep.lu.se/
    30723072
    30733073  BASE is free software; you can redistribute it and/or
  • branches/3.18-stable/doc/src/docbook/developer/documentation.xml

    r6576 r7978  
    13521352<xref linkend="docbook.usedtags.links" />
    13531353<link linkend="docbook.usedtags.links">Link to this section</link>
    1354 <ulink url="http://base.thep.lu.se">Base2's homepage</ulink>
     1354<ulink url="https://base.thep.lu.se">Base2's homepage</ulink>
    13551355]]>
    13561356</programlisting>
     
    18571857    <para>
    18581858      Existing Javadoc documentation is available on-line at:
    1859       <ulink url="http://base.thep.lu.se/chrome/site/doc/api/index.html"
    1860         >http://base.thep.lu.se/chrome/site/doc/api/index.html</ulink>.
     1859      <ulink url="https://base.thep.lu.se/chrome/site/doc/api/index.html"
     1860        >https://base.thep.lu.se/chrome/site/doc/api/index.html</ulink>.
    18611861    </para>
    18621862   
  • branches/3.18-stable/doc/src/docbook/developer/extensions.xml

    r7915 r7978  
    8181        The code examples in this chapter can be downloaded from the
    8282        BASE plug-ins site:
    83         <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode"
    84         >http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode</ulink>
     83        <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode"
     84        >https://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode</ulink>
    8585      </para>
    8686    </sect2>
     
    19431943        BASE doesn't ship with any service, but there is an FTP service
    19441944        available at the BASE plug-ins site: <ulink
    1945         url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp">
    1946         http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp</ulink>
     1945        url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp">
     1946        https://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp</ulink>
    19471947      </para>
    19481948    </sect2>
     
    19911991        The BASE plug-ins site has an connection manager that support
    19921992        external files via FTP and SFTP: <ulink
    1993         url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles">
    1994         http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles</ulink>
     1993        url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles">
     1994        https://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles</ulink>
    19951995      </para>
    19961996     
     
    24862486        factory that can be used without coding if the added column can be expressed as a property path that
    24872487        can be handled by the <classname docapi="net.sf.basedb.core">Metadata</classname> class.
    2488         As usual, see the <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode">example code</ulink>
     2488        As usual, see the <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode">example code</ulink>
    24892489        for some examples.
    24902490      </para>
     
    25162516        extension with a custom column that uses the <code>!x.</code> prefix
    25172517        as the column id. Here is an example from the Variant Search extension
    2518         (<ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.varsearch"
    2519         >http://baseplugins.thep.lu.se/wiki/net.sf.basedb.varsearch</ulink>):
     2518        (<ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.varsearch"
     2519        >https://baseplugins.thep.lu.se/wiki/net.sf.basedb.varsearch</ulink>):
    25202520      </para>
    25212521     
     
    26032603          login with some other method. Examples of actual implementations can be found in the
    26042604          the <ulink
    2605           url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.yubikey">YubiKey</ulink>
     2605          url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.yubikey">YubiKey</ulink>
    26062606          and <ulink
    2607           url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.otp">OTP</ulink> extensions.
     2607          url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.otp">OTP</ulink> extensions.
    26082608        </para>
    26092609       
  • branches/3.18-stable/doc/src/docbook/developer/migrate_2_3.xml

    r6576 r7978  
    5252    <itemizedlist>
    5353      <listitem>
    54         <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/html/index.html">http://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>:
     54        <para><ulink url="https://base.thep.lu.se/chrome/site/2.17/html/index.html">https://base.thep.lu.se/chrome/site/2.17/html/index.html</ulink>:
    5555        User manual.
    5656        </para>
    5757      </listitem>
    5858      <listitem>
    59         <para><ulink url="http://base.thep.lu.se/chrome/site/2.17/api/index.html">http://base.thep.lu.se/chrome/site/2.17/api/index.html</ulink>:
     59        <para><ulink url="https://base.thep.lu.se/chrome/site/2.17/api/index.html">https://base.thep.lu.se/chrome/site/2.17/api/index.html</ulink>:
    6060        API documentation.
    6161        </para>
     
    133133      You'll need to make sure that your build system can handle this.
    134134      The BASE JAR files can be downloaded from
    135       <ulink url="http://base.thep.lu.se/chrome/site/files/base/jars/">http://base.thep.lu.se/chrome/site/files/base/jars/</ulink>.
     135      <ulink url="https://base.thep.lu.se/chrome/site/files/base/jars/">https://base.thep.lu.se/chrome/site/files/base/jars/</ulink>.
    136136    </note>
    137137   
     
    170170          Additionally, several other items implement the new <interfacename
    171171          docapi="net.sf.basedb.core">Subtypable</interfacename> interface.
    172           See <ulink url="http://base.thep.lu.se/ticket/1597">ticket #1597 (Subtypes of items)</ulink>
     172          See <ulink url="https://base.thep.lu.se/ticket/1597">ticket #1597 (Subtypes of items)</ulink>
    173173          for more information.
    174174        </para>
     
    189189          converted to a physical bioassay in BASE 3 with the subtype 'Hybridization'. The
    190190          server admin can define additional subtypes. See
    191           <ulink url="http://base.thep.lu.se/ticket/1153">ticket #1153 (Handling short read
     191          <ulink url="https://base.thep.lu.se/ticket/1153">ticket #1153 (Handling short read
    192192          transcript sequence data)</ulink> for more information.
    193193         
     
    212212          <xref linkend="extensions_developer.fileset_validator"/> and
    213213          <ulink
    214           url="http://base.thep.lu.se/ticket/1598">ticket #1598 (Use
     214          url="https://base.thep.lu.se/ticket/1598">ticket #1598 (Use
    215215          the extensions system for data file validators and metadata readers)</ulink> for more information.
    216216        </para>
     
    222222          store more than one file for each <classname docapi="net.sf.basedb.core">DataFileType</classname>
    223223          which was not possible before. The API for adding files have changed.
    224           See <ulink url="http://base.thep.lu.se/ticket/1604">ticket #1604
     224          See <ulink url="https://base.thep.lu.se/ticket/1604">ticket #1604
    225225          (Support for multiple files of the same type in a FileSet)</ulink> for
    226226          more information.
     
    235235          make it possible to get information about the main zip/tar file that is being
    236236          unpacked. See <ulink
    237           url="http://base.thep.lu.se/ticket/978">ticket #978 (Unzipped files never inherit
     237          url="https://base.thep.lu.se/ticket/978">ticket #978 (Unzipped files never inherit
    238238          file type specified during upload)</ulink> for more information.
    239239        </para>
     
    248248          a moderate computer today. If additional security is needed we recommend that
    249249          BASE is installed with HTTPS access only. See <ulink
    250           url="http://base.thep.lu.se/ticket/1641">ticket #1641 (Use bcrypt for storing
     250          url="https://base.thep.lu.se/ticket/1641">ticket #1641 (Use bcrypt for storing
    251251          passwords instead of MD5)</ulink> for more information.
    252252        </para>
     
    300300          <xref linkend="plugins.installation" /> and
    301301          <ulink
    302           url="http://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation
     302          url="https://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation
    303303          procedure for plug-ins, extensions and more...)</ulink> for more information.
    304304        </para>
     
    311311          JAR file. The <property>Class-Path</property> attribute in <filename>META-INF/MANIFEST.MF</filename>
    312312          must still be set. See <xref linkend="plugin_developer.organize"/> and <ulink
    313           url="http://base.thep.lu.se/ticket/1594">ticket #1594 (JarClassLoader support for JARs within JARs)</ulink>.
     313          url="https://base.thep.lu.se/ticket/1594">ticket #1594 (JarClassLoader support for JARs within JARs)</ulink>.
    314314        </para>
    315315      </listitem>
  • branches/3.18-stable/doc/src/docbook/developer/overview.xml

    r6465 r7978  
    455455        <listitem>
    456456          <para>
    457           The <ulink url="http://baseplugins.thep.lu.se">BASE plug-ins site</ulink> also
     457          The <ulink url="https://baseplugins.thep.lu.se">BASE plug-ins site</ulink> also
    458458          has examples of extensions.
    459459          </para>
  • branches/3.18-stable/doc/src/docbook/developer/plugins.xml

    r7598 r7978  
    37273727        since code doesn't have to be installed in the
    37283728        WEB-INF/lib or WEB-INF/classes directory. See <ulink
    3729         url="http://base.thep.lu.se/ticket/1600">ticket #1600: Convert file
     3729        url="https://base.thep.lu.se/ticket/1600">ticket #1600: Convert file
    37303730        packing plug-in system to an extension point</ulink> for more information.
    37313731        </para>
     
    40214021      You can download a tar file with the source and compiled plug-in code from
    40224022      the BASE plug-ins website:
    4023       <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode"
    4024       >http://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode</ulink>
     4023      <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode"
     4024      >https://baseplugins.thep.lu.se/wiki/net.sf.basedb.examplecode</ulink>
    40254025    </para>
    40264026   
  • branches/3.18-stable/doc/src/docbook/faq/faqs.xml

    r5820 r7978  
    453453                <para>
    454454                Submit a ticket through
    455                 <ulink url="http://base.thep.lu.se">http://base.thep.lu.se</ulink>
     455                <ulink url="https://base.thep.lu.se">https://base.thep.lu.se</ulink>
    456456                explaining what you'd like to see with respect to to CDT and CAB files.
    457457                </para>
     
    477477            <para>
    478478              Yes, but not by default. There is
    479               an <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina
     479              an <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina
    480480              package</ulink> that provides Illumina support to
    481481              BASE. The package is straightforward to install, visit
     
    526526              though even though this might depend on your set-up...)
    527527              The plug-in is not included in a standard BASE installation, but
    528               can be downloaded from the <ulink url="http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix"
     528              can be downloaded from the <ulink url="https://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix"
    529529                >BASE plug-ins web site</ulink>.
    530530            </para>
  • branches/3.18-stable/doc/src/docbook/overview/features.xml

    r6465 r7978  
    158158      of tools are pre-installed with BASE, and optional plug-ins can
    159159      be downloaded from the <ulink
    160       url="http://baseplugins.thep.lu.se">BASE plug-in site
     160      url="https://baseplugins.thep.lu.se">BASE plug-in site
    161161      </ulink>. BASE capitalise from other software tools, such as
    162162      MEV, by integrating them into the user interface. Such
     
    257257      BASE comes with a specific Affymetrix platform and Illumina can
    258258      be supported by customising BASE (go to the <ulink
    259       url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     259      url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    260260      Illumina package</ulink> web site for more information on adding
    261261      Illumina support to BASE).
     
    335335              platform support is not included in a standard BASE
    336336              installation but there is a <ulink
    337               url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     337              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    338338              Illumina package</ulink> available for seamless
    339339              integration of the Illumina array platform to BASE.
     
    472472              Not available in BASE directly but it is added with the
    473473              <ulink
    474               url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     474              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    475475              Illumina plug-in</ulink> that adds Illumina array
    476476              platform support to BASE.
  • branches/3.18-stable/doc/src/docbook/overview/resources.xml

    r6576 r7978  
    3838    <para>
    3939      The BASE project site is located at
    40       <ulink url='http://base.thep.lu.se'>http://base.thep.lu.se</ulink>.
     40      <ulink url='https://base.thep.lu.se'>https://base.thep.lu.se</ulink>.
    4141      Here is a lot of useful information about the project and the program, e.g.
    4242      documentation/manuals, download-pages, contact information and much more. The most
     
    4848        The download page is accessed from the download section, on the home page, by
    4949        following the link to
    50         <guilabel><ulink url='http://base.thep.lu.se/wiki/DownloadPage'
     50        <guilabel><ulink url='https://base.thep.lu.se/wiki/DownloadPage'
    5151          >Download Page</ulink></guilabel>.
    5252        From this page you can download BASE releases as packaged tar.gz
     
    110110        A ticket is a note about a bug or a new feature that has not yet been
    111111        implemented. To show the list of outstanding tickets use the
    112         <guibutton><ulink url="http://base.thep.lu.se/query"
     112        <guibutton><ulink url="https://base.thep.lu.se/query"
    113113          >View Tickets</ulink></guibutton> button on BASE web site.
    114114        It is a good idea to have a look at this list before reporting a bug
     
    131131      <para>
    132132        The roadmap of BASE is accessed from the
    133         <guibutton><ulink url="http://base.thep.lu.se/roadmap"
     133        <guibutton><ulink url="https://base.thep.lu.se/roadmap"
    134134          >Roadmap</ulink></guibutton> button on the home page. This page
    135135        contains information about the plans for future development, including
     
    197197      Plug-ins which are not included in the installation of BASE, have their own site,
    198198      called
    199       <ulink url="http://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
     199      <ulink url="https://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
    200200      which includes a download page for submitted none-core plug-ins.     
    201201      Here is also information how to become a plug-in developer, with
     
    211211      explore BASE without having to install it. Follow the link on
    212212      BASE web site to the demo server or go directly to
    213       <ulink url="http://base.onk.lu.se/demo/">
    214         http://base.onk.lu.se/demo/
     213      <ulink url="https://base.onk.lu.se/demo/">
     214        https://base.onk.lu.se/demo/
    215215      </ulink>. NOTE! The demo server is currently down!
    216216    </para>
     
    229229    <para>
    230230      BASE project has three different mailing lists available for subscription. Visit the
    231       <ulink url="http://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
     231      <ulink url="https://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
    232232      to get more information about each one of the mailing lists. All posted mails are saved
    233233      in an archive for each list, it can therefore be a good idea to have a look here before
  • branches/3.18-stable/doc/src/docbook/overview/why_base.xml

    r5844 r7978  
    104104      BASE. This implies interplay with adopting the BASE software
    105105      (the <ulink
    106       url='http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
     106      url='https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
    107107      extension</ulink> is an example of adaptation on BASE to
    108108      specific needs in SCAN-B) and the laboratory work to achieve
  • branches/3.18-stable/doc/src/docbook/user/file_system.xml

    r7598 r7978  
    635635                On this tab you may specify options for SSH connections. BASE has not
    636636                built-in support for SSH but this can be enabled via plug-ins.
    637                 See the <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles">External
     637                See the <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles">External
    638638                files support</ulink> extension package.
    639639              </para>
  • branches/3.18-stable/doc/src/docbook/user/webclient.xml

    r7959 r7978  
    4747        <para>
    4848          You may, for example, try the BASE demo server. Go to the
    49           URL <ulink url="http://base.onk.lu.se/demo/">http://base.onk.lu.se/demo/</ulink>
     49          URL <ulink url="https://base.onk.lu.se/demo/">https://base.onk.lu.se/demo/</ulink>
    5050          and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput>
    5151          for the password. NOTE! The demo server is currently down!
  • branches/3.18-stable/doc/src/javadoc/overview.html

    r5818 r7978  
    3030  or plug-in developers. We guarantee a certain degree of stability
    3131  among the classes and methods in the public API. See documentation
    32   on the <a href="http://base.thep.lu.se/chrome/site/doc/docbook/html/developerdoc/api/api_overview.html"
     32  on the <a href="https://base.thep.lu.se/chrome/site/doc/docbook/html/developerdoc/api/api_overview.html"
    3333    >BASE web site</a> for more information.
    3434  Methods that have been tagged as <code>@deprecated</code> should be considered
  • branches/3.18-stable/doc/test/performance/index.html

    r4889 r7978  
    44
    55  Copyright (C) 2007 Nicklas Nordborg
    6   Copyright (C) 2008 Jari Häkkinen
     6  Copyright (C) 2008 Jari Hkkinen
    77
    88  This file is part of BASE - BioArray Software Environment.
     
    7878    make them publicly available for download. To get the test file you need to be a
    7979    core developer. Read the instructions on the
    80     <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
     80    <a href="https://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
    8181    page, <code>Test data</code> section on the Base 2 web site.
    8282  </p>
  • branches/3.18-stable/doc/test/roles/index.html

    r7052 r7978  
    143143    make them publicly available for download. To get the test file you need to be a
    144144    core developer. Read the instructions on the
    145     <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
     145    <a href="https://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
    146146    page, <code>Test data</code> section on the BASE web site. The automated
    147147    test programs require that file are placed (checked out) in the 'testdata'
  • branches/3.18-stable/src/clients/web/web-extensions.xml

    r7850 r7978  
    3535    <copyright>BASE development team</copyright>
    3636    <email>basedb-users@lists.sourceforge.net</email>
    37     <url>http://base.thep.lu.se/</url>
     37    <url>https://base.thep.lu.se/</url>
    3838  </about>
    3939 
  • branches/3.18-stable/src/core/core-extensions.xml

    r7895 r7978  
    3535    <copyright>BASE development team</copyright>
    3636    <email>basedb-users@lists.sourceforge.net</email>
    37     <url>http://base.thep.lu.se/</url>
     37    <url>https://base.thep.lu.se/</url>
    3838  </about>
    3939 
  • branches/3.18-stable/src/plugins/core/core-plugins.xml

    r7849 r7978  
    3434    <copyright>BASE development team</copyright>
    3535    <email>basedb-users@lists.sourceforge.net</email>
    36     <url>http://base.thep.lu.se/</url>
     36    <url>https://base.thep.lu.se/</url>
    3737  </about>
    3838 
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