Changeset 7978
- Timestamp:
- Jun 11, 2021, 12:51:05 PM (20 months ago)
- Location:
- branches/3.18-stable
- Files:
-
- 32 edited
Legend:
- Unmodified
- Added
- Removed
-
branches/3.18-stable/doc/historical/admin/extended-properties.html
r4889 r7978 4 4 $Id$ 5 5 6 Copyright (C) 2006 Jari H äkkinen, Nicklas Nordborg7 Copyright (C) 2007 Jari H äkkinen6 Copyright (C) 2006 Jari H�kkinen, Nicklas Nordborg 7 Copyright (C) 2007 Jari H�kkinen 8 8 9 9 This file is part of BASE - BioArray Software Environment. … … 60 60 for ExtendableData</a> </li> 61 61 <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> 63 63 </ul> 64 64 … … 110 110 The 111 111 <a 112 href= http://base.thep.lu.se/browser/trunk/config/dist/extended-properties.xml>default112 href="https://base.thep.lu.se/browser/trunk/config/dist/extended-properties.xml">default 113 113 extended properties</a> file. The properties described in 114 114 this sample file is required when migration from BASE 1.2 … … 124 124 A 125 125 <a 126 href= http://base.thep.lu.se/browser/trunk/misc/config/minimalistic_extended-properties.xml>minimalistic126 href="https://base.thep.lu.se/browser/trunk/misc/config/minimalistic_extended-properties.xml">minimalistic 127 127 setup</a>. This is useful when, at BASE installation time, 128 128 it is not known what reporter data will be stored in the … … 146 146 to follow the straightforward format of 147 147 <a 148 href= http://base.thep.lu.se/browser/trunk/src/extended-properties.xml>default148 href="https://base.thep.lu.se/browser/trunk/src/extended-properties.xml">default 149 149 extended properties</a>. The problem is that some knowledge of 150 150 the underlying database schema is needed. -
branches/3.18-stable/doc/historical/admin/plugin_configuration/coreplugins.html
r4889 r7978 3 3 $Id$ 4 4 5 Copyright (C) 2007 Jari H äkkinen, Peter Johansson, Martin Svensson5 Copyright (C) 2007 Jari H�kkinen, Peter Johansson, Martin Svensson 6 6 7 7 This file is part of BASE - BioArray Software Environment. … … 39 39 <p> 40 40 This document is mostly superseeded by the <a 41 href="http ://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html">core41 href="https://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html">core 42 42 plugins list in the BASE 2 documentation</a>. Some tools are 43 43 still listed here. … … 51 51 <p class="authors"> 52 52 <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. 54 54 </p> 55 55 </div> -
branches/3.18-stable/doc/historical/development/build.html
r5656 r7978 41 41 <div class="warning"> 42 42 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> 44 44 </div> 45 45 … … 90 90 </p> 91 91 <pre class="code"> 92 svn checkout http ://base.thep.lu.se/svn/trunk/ base92 svn checkout https://base.thep.lu.se/svn/trunk/ base 93 93 </pre> 94 94 … … 99 99 For information about how to get other version, including specific releases and bugfix 100 100 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> 103 103 directly. 104 104 </p> -
branches/3.18-stable/doc/historical/development/plugins/index.html
r4889 r7978 3 3 $Id$ 4 4 5 Copyright (C) 2006 Jari H äkkinen, Nicklas Nordborg5 Copyright (C) 2006 Jari H�kkinen, Nicklas Nordborg 6 6 7 7 This file is part of BASE - BioArray Software Environment. … … 124 124 null, 125 125 "base@thep.lu.se", 126 "http ://base.thep.lu.se"126 "https://base.thep.lu.se" 127 127 ); 128 128 -
branches/3.18-stable/doc/historical/test/index.html
r4889 r7978 4 4 $Id$ 5 5 6 Copyright (C) 2006 Jari H äkkinen, Nicklas Nordborg6 Copyright (C) 2006 Jari H�kkinen, Nicklas Nordborg 7 7 8 8 This file is part of BASE - BioArray Software Environment. … … 71 71 target="_new">basedb-devel archive</a>) for discussions about 72 72 BASE 2.0. Please use the <a 73 href= http://www.edgewall.com/trac/>trac</a> based73 href="http://www.edgewall.com/trac/">trac</a> based 74 74 reporting system for bug reports, enhancement ideas, and feature 75 75 requests. More information at <a 76 href= http://base.thep.lu.se/#Feedback>the feedback section</a> of77 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>. 78 78 </p> 79 79 -
branches/3.18-stable/doc/historical/test/merge/index.html
r4509 r7978 71 71 <b>See also</b><br> 72 72 <ol> 73 <li><a href="http ://base.thep.lu.se/ticket/215">Ticket #215: Incorrect use of73 <li><a href="https://base.thep.lu.se/ticket/215">Ticket #215: Incorrect use of 74 74 DynamicSpotQuery in table view, plot function, filter function, etc.</a> 75 75 </ol> -
branches/3.18-stable/doc/historical/user/getting_started.html
r4889 r7978 4 4 $Id$ 5 5 6 Copyright (C) 2006 Jari H äkkinen6 Copyright (C) 2006 Jari H�kkinen 7 7 8 8 This file is part of BASE - BioArray Software Environment. … … 103 103 other works out of the box. Some external plug-ins as the 104 104 <a 105 href= http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress105 href="https://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress">RMAExpress 106 106 plug-in for BASE</a> has to be compiled before including 107 107 them into your BASE server.</p> … … 442 442 <p> (Affymetrix only) <b>Install 443 443 <a name=RMAExpressInstall 444 href= http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress>RMAExpress444 href="https://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress">RMAExpress 445 445 plug-in for BASE</a></b> <br> This plug-in is required for 446 446 Affymetrix data. The plug-in will create a bioassay set, … … 650 650 BASE. We have not covered how to use the LIMS part of BASE, nor 651 651 annotations, and much more. We are creating documentation, please 652 browse <a href= http://base.thep.lu.se/>BASE web site</a> for the652 browse <a href="https://base.thep.lu.se/">BASE web site</a> for the 653 653 latest available documents. </p> 654 654 -
branches/3.18-stable/doc/src/docbook/admin/installation.xml
r7916 r7978 157 157 This option is for advanced users only and is not 158 158 covered here. Please refer to 159 <ulink url="http ://base.thep.lu.se/wiki/BuildingBase" /> for information on159 <ulink url="https://base.thep.lu.se/wiki/BuildingBase" /> for information on 160 160 this download option. 161 161 </para> … … 420 420 <para> 421 421 <ulink 422 url="http ://base.thep.lu.se/wiki/DownloadPage">Download422 url="https://base.thep.lu.se/wiki/DownloadPage">Download 423 423 BASE</ulink> and unpack the downloaded file, 424 424 i.e. <command>tar zxpf base-...tar.gz</command>. If you … … 426 426 a checkout of the source from the subversion repository 427 427 (subversion checkout instructions at 428 <ulink url="http ://base.thep.lu.se/wiki/DownloadPage">BASE428 <ulink url="https://base.thep.lu.se/wiki/DownloadPage">BASE 429 429 trac site</ulink>). 430 430 </para> … … 451 451 is available in the 452 452 <ulink 453 url="http ://base.thep.lu.se/wiki/BuildingBase">building453 url="https://base.thep.lu.se/wiki/BuildingBase">building 454 454 BASE document</ulink>. When you return back after 455 455 compiling in the subversion tree you can follow the … … 530 530 There is an 531 531 administrator <ulink 532 url="http ://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document532 url="https://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document 533 533 discussing extended properties</ulink> available. If you 534 534 plan to perform a migration of a BASE version 1.2 database you … … 906 906 downloads at 907 907 <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> 909 909 </para> 910 910 </listitem> … … 1363 1363 BASE version on the BASE web site, 1364 1364 <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>. 1367 1367 1368 1368 If you want the documentation for a specific version you will … … 1390 1390 perhaps other feedback that concerns the program. As default 1391 1391 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>. 1393 1393 Note that users must login in order to submit information. 1394 1394 </para> -
branches/3.18-stable/doc/src/docbook/appendix/base.config.xml
r7598 r7978 829 829 If you want to setup your own test environment with a https server that only 830 830 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> 833 833 </para> 834 834 -
branches/3.18-stable/doc/src/docbook/appendix/coreplugins.xml
r7640 r7978 42 42 <para> 43 43 Contributed plug-ins are available at <ulink 44 url="http ://baseplugins.thep.lu.se" >http://baseplugins.thep.lu.se44 url="https://baseplugins.thep.lu.se" >https://baseplugins.thep.lu.se 45 45 </ulink>. These plug-ins are either developed outside the core team 46 46 or require external non-Java compilers and tools. These packages -
branches/3.18-stable/doc/src/docbook/appendix/incompatible.xml
r7681 r7978 201 201 other clients that use a different client id are affected and may stop to work 202 202 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>. 204 204 </para> 205 205 … … 345 345 event handlers and script sections since this is a possible entry 346 346 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>). 348 348 Extension developers are encouraged to make the same changes in 349 349 their applications. … … 469 469 for the best user experience. The changes are too numerous so we can't 470 470 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">ticket471 information is needed or see <ulink url="https://base.thep.lu.se/ticket/1655">ticket 472 472 1655</ulink> for some screenshots and other information. 473 473 </para> … … 484 484 may cause problems for code that is expecting all annotations to be 485 485 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> 487 487 for more information. 488 488 </para> … … 497 497 this situation. Particulary, infinite loops must be avoided when traversing the "parent" 498 498 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> 500 500 for more information. 501 501 </para> … … 520 520 <para> 521 521 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" 523 523 >BASE 2.17 documentation</ulink>. 524 524 </para> -
branches/3.18-stable/doc/src/docbook/appendix/update_warnings.xml
r7916 r7978 571 571 We only support updating to BASE 3 from BASE 2.17. If you have an older BASE 572 572 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">BASE573 BASE 2.17 can be downloaded from the <ulink url="https://base.thep.lu.se/wiki/DownloadPage">BASE 574 574 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>. 577 577 </para> 578 578 -
branches/3.18-stable/doc/src/docbook/appendix/web.xml.xml
r7609 r7978 64 64 of a POST request instead. This functionality can disabled by 65 65 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>. 67 67 </para> 68 68 </listitem> -
branches/3.18-stable/doc/src/docbook/developer/base_api.xml
r7640 r7978 2499 2499 This documentation is only available in the old format which may not be up-to-date with 2500 2500 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> 2503 2503 </para> 2504 2504 </sect2> … … 2509 2509 This documentation is only available in the old format which may not be up-to-date with 2510 2510 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> 2513 2513 </para> 2514 2514 </sect2> … … 2531 2531 This documentation is only available in the old format which may not be up-to-date with 2532 2532 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> 2535 2535 </para> 2536 2536 </sect2> … … 2540 2540 This documentation is only available in the old format which may not be up-to-date with 2541 2541 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> 2544 2544 </para> 2545 2545 </sect2> … … 2556 2556 This documentation is only available in the old format which may not be up-to-date with 2557 2557 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> 2560 2560 </para> 2561 2561 </sect2> … … 3161 3161 This documentation is only available in the old format which may not be up-to-date with 3162 3162 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> 3165 3165 </para> 3166 3166 … … 3173 3173 This documentation is only available in the old format which may not be up-to-date with 3174 3174 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> 3177 3177 </para> 3178 3178 </sect1> -
branches/3.18-stable/doc/src/docbook/developer/core_ref.xml
r6912 r7978 31 31 <title>Publishing a new release</title> 32 32 <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>. 34 34 </para> 35 35 </sect1> … … 38 38 <title>Subversion / building BASE</title> 39 39 <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>. 41 41 </para> 42 42 </sect1> … … 586 586 587 587 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/ 589 589 590 590 BASE is free software; you can redistribute it and/or … … 3069 3069 3070 3070 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/ 3072 3072 3073 3073 BASE is free software; you can redistribute it and/or -
branches/3.18-stable/doc/src/docbook/developer/documentation.xml
r6576 r7978 1352 1352 <xref linkend="docbook.usedtags.links" /> 1353 1353 <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> 1355 1355 ]]> 1356 1356 </programlisting> … … 1857 1857 <para> 1858 1858 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>. 1861 1861 </para> 1862 1862 -
branches/3.18-stable/doc/src/docbook/developer/extensions.xml
r7915 r7978 81 81 The code examples in this chapter can be downloaded from the 82 82 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> 85 85 </para> 86 86 </sect2> … … 1943 1943 BASE doesn't ship with any service, but there is an FTP service 1944 1944 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> 1947 1947 </para> 1948 1948 </sect2> … … 1991 1991 The BASE plug-ins site has an connection manager that support 1992 1992 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> 1995 1995 </para> 1996 1996 … … 2486 2486 factory that can be used without coding if the added column can be expressed as a property path that 2487 2487 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> 2489 2489 for some examples. 2490 2490 </para> … … 2516 2516 extension with a custom column that uses the <code>!x.</code> prefix 2517 2517 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>): 2520 2520 </para> 2521 2521 … … 2603 2603 login with some other method. Examples of actual implementations can be found in the 2604 2604 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> 2606 2606 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. 2608 2608 </para> 2609 2609 -
branches/3.18-stable/doc/src/docbook/developer/migrate_2_3.xml
r6576 r7978 52 52 <itemizedlist> 53 53 <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>: 55 55 User manual. 56 56 </para> 57 57 </listitem> 58 58 <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>: 60 60 API documentation. 61 61 </para> … … 133 133 You'll need to make sure that your build system can handle this. 134 134 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>. 136 136 </note> 137 137 … … 170 170 Additionally, several other items implement the new <interfacename 171 171 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> 173 173 for more information. 174 174 </para> … … 189 189 converted to a physical bioassay in BASE 3 with the subtype 'Hybridization'. The 190 190 server admin can define additional subtypes. See 191 <ulink url="http ://base.thep.lu.se/ticket/1153">ticket #1153 (Handling short read191 <ulink url="https://base.thep.lu.se/ticket/1153">ticket #1153 (Handling short read 192 192 transcript sequence data)</ulink> for more information. 193 193 … … 212 212 <xref linkend="extensions_developer.fileset_validator"/> and 213 213 <ulink 214 url="http ://base.thep.lu.se/ticket/1598">ticket #1598 (Use214 url="https://base.thep.lu.se/ticket/1598">ticket #1598 (Use 215 215 the extensions system for data file validators and metadata readers)</ulink> for more information. 216 216 </para> … … 222 222 store more than one file for each <classname docapi="net.sf.basedb.core">DataFileType</classname> 223 223 which was not possible before. The API for adding files have changed. 224 See <ulink url="http ://base.thep.lu.se/ticket/1604">ticket #1604224 See <ulink url="https://base.thep.lu.se/ticket/1604">ticket #1604 225 225 (Support for multiple files of the same type in a FileSet)</ulink> for 226 226 more information. … … 235 235 make it possible to get information about the main zip/tar file that is being 236 236 unpacked. See <ulink 237 url="http ://base.thep.lu.se/ticket/978">ticket #978 (Unzipped files never inherit237 url="https://base.thep.lu.se/ticket/978">ticket #978 (Unzipped files never inherit 238 238 file type specified during upload)</ulink> for more information. 239 239 </para> … … 248 248 a moderate computer today. If additional security is needed we recommend that 249 249 BASE is installed with HTTPS access only. See <ulink 250 url="http ://base.thep.lu.se/ticket/1641">ticket #1641 (Use bcrypt for storing250 url="https://base.thep.lu.se/ticket/1641">ticket #1641 (Use bcrypt for storing 251 251 passwords instead of MD5)</ulink> for more information. 252 252 </para> … … 300 300 <xref linkend="plugins.installation" /> and 301 301 <ulink 302 url="http ://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation302 url="https://base.thep.lu.se/ticket/1592">ticket #1592 (Unified installation 303 303 procedure for plug-ins, extensions and more...)</ulink> for more information. 304 304 </para> … … 311 311 JAR file. The <property>Class-Path</property> attribute in <filename>META-INF/MANIFEST.MF</filename> 312 312 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>. 314 314 </para> 315 315 </listitem> -
branches/3.18-stable/doc/src/docbook/developer/overview.xml
r6465 r7978 455 455 <listitem> 456 456 <para> 457 The <ulink url="http ://baseplugins.thep.lu.se">BASE plug-ins site</ulink> also457 The <ulink url="https://baseplugins.thep.lu.se">BASE plug-ins site</ulink> also 458 458 has examples of extensions. 459 459 </para> -
branches/3.18-stable/doc/src/docbook/developer/plugins.xml
r7598 r7978 3727 3727 since code doesn't have to be installed in the 3728 3728 WEB-INF/lib or WEB-INF/classes directory. See <ulink 3729 url="http ://base.thep.lu.se/ticket/1600">ticket #1600: Convert file3729 url="https://base.thep.lu.se/ticket/1600">ticket #1600: Convert file 3730 3730 packing plug-in system to an extension point</ulink> for more information. 3731 3731 </para> … … 4021 4021 You can download a tar file with the source and compiled plug-in code from 4022 4022 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> 4025 4025 </para> 4026 4026 -
branches/3.18-stable/doc/src/docbook/faq/faqs.xml
r5820 r7978 453 453 <para> 454 454 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> 456 456 explaining what you'd like to see with respect to to CDT and CAB files. 457 457 </para> … … 477 477 <para> 478 478 Yes, but not by default. There is 479 an <ulink url="http ://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina479 an <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina 480 480 package</ulink> that provides Illumina support to 481 481 BASE. The package is straightforward to install, visit … … 526 526 though even though this might depend on your set-up...) 527 527 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" 529 529 >BASE plug-ins web site</ulink>. 530 530 </para> -
branches/3.18-stable/doc/src/docbook/overview/features.xml
r6465 r7978 158 158 of tools are pre-installed with BASE, and optional plug-ins can 159 159 be downloaded from the <ulink 160 url="http ://baseplugins.thep.lu.se">BASE plug-in site160 url="https://baseplugins.thep.lu.se">BASE plug-in site 161 161 </ulink>. BASE capitalise from other software tools, such as 162 162 MEV, by integrating them into the user interface. Such … … 257 257 BASE comes with a specific Affymetrix platform and Illumina can 258 258 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"> 260 260 Illumina package</ulink> web site for more information on adding 261 261 Illumina support to BASE). … … 335 335 platform support is not included in a standard BASE 336 336 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"> 338 338 Illumina package</ulink> available for seamless 339 339 integration of the Illumina array platform to BASE. … … 472 472 Not available in BASE directly but it is added with the 473 473 <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"> 475 475 Illumina plug-in</ulink> that adds Illumina array 476 476 platform support to BASE. -
branches/3.18-stable/doc/src/docbook/overview/resources.xml
r6576 r7978 38 38 <para> 39 39 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>. 41 41 Here is a lot of useful information about the project and the program, e.g. 42 42 documentation/manuals, download-pages, contact information and much more. The most … … 48 48 The download page is accessed from the download section, on the home page, by 49 49 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' 51 51 >Download Page</ulink></guilabel>. 52 52 From this page you can download BASE releases as packaged tar.gz … … 110 110 A ticket is a note about a bug or a new feature that has not yet been 111 111 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" 113 113 >View Tickets</ulink></guibutton> button on BASE web site. 114 114 It is a good idea to have a look at this list before reporting a bug … … 131 131 <para> 132 132 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" 134 134 >Roadmap</ulink></guibutton> button on the home page. This page 135 135 contains information about the plans for future development, including … … 197 197 Plug-ins which are not included in the installation of BASE, have their own site, 198 198 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> 200 200 which includes a download page for submitted none-core plug-ins. 201 201 Here is also information how to become a plug-in developer, with … … 211 211 explore BASE without having to install it. Follow the link on 212 212 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/ 215 215 </ulink>. NOTE! The demo server is currently down! 216 216 </para> … … 229 229 <para> 230 230 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> 232 232 to get more information about each one of the mailing lists. All posted mails are saved 233 233 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 104 104 BASE. This implies interplay with adopting the BASE software 105 105 (the <ulink 106 url='http ://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie106 url='https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie 107 107 extension</ulink> is an example of adaptation on BASE to 108 108 specific needs in SCAN-B) and the laboratory work to achieve -
branches/3.18-stable/doc/src/docbook/user/file_system.xml
r7598 r7978 635 635 On this tab you may specify options for SSH connections. BASE has not 636 636 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">External637 See the <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles">External 638 638 files support</ulink> extension package. 639 639 </para> -
branches/3.18-stable/doc/src/docbook/user/webclient.xml
r7959 r7978 47 47 <para> 48 48 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> 50 50 and enter <userinput>base2</userinput> for the login and <userinput>base2</userinput> 51 51 for the password. NOTE! The demo server is currently down! -
branches/3.18-stable/doc/src/javadoc/overview.html
r5818 r7978 30 30 or plug-in developers. We guarantee a certain degree of stability 31 31 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" 33 33 >BASE web site</a> for more information. 34 34 Methods that have been tagged as <code>@deprecated</code> should be considered -
branches/3.18-stable/doc/test/performance/index.html
r4889 r7978 4 4 5 5 Copyright (C) 2007 Nicklas Nordborg 6 Copyright (C) 2008 Jari H äkkinen6 Copyright (C) 2008 Jari H�kkinen 7 7 8 8 This file is part of BASE - BioArray Software Environment. … … 78 78 make them publicly available for download. To get the test file you need to be a 79 79 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> 81 81 page, <code>Test data</code> section on the Base 2 web site. 82 82 </p> -
branches/3.18-stable/doc/test/roles/index.html
r7052 r7978 143 143 make them publicly available for download. To get the test file you need to be a 144 144 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> 146 146 page, <code>Test data</code> section on the BASE web site. The automated 147 147 test programs require that file are placed (checked out) in the 'testdata' -
branches/3.18-stable/src/clients/web/web-extensions.xml
r7850 r7978 35 35 <copyright>BASE development team</copyright> 36 36 <email>basedb-users@lists.sourceforge.net</email> 37 <url>http ://base.thep.lu.se/</url>37 <url>https://base.thep.lu.se/</url> 38 38 </about> 39 39 -
branches/3.18-stable/src/core/core-extensions.xml
r7895 r7978 35 35 <copyright>BASE development team</copyright> 36 36 <email>basedb-users@lists.sourceforge.net</email> 37 <url>http ://base.thep.lu.se/</url>37 <url>https://base.thep.lu.se/</url> 38 38 </about> 39 39 -
branches/3.18-stable/src/plugins/core/core-plugins.xml
r7849 r7978 34 34 <copyright>BASE development team</copyright> 35 35 <email>basedb-users@lists.sourceforge.net</email> 36 <url>http ://base.thep.lu.se/</url>36 <url>https://base.thep.lu.se/</url> 37 37 </about> 38 38
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