MediaWiki/Installation/v5 - Revision history

AngelHerraez at 19:13, 15 January 2025

2025-01-15T19:13:03Z

AngelHerraez: updating links for v6

2025-01-15T19:12:01Z

updating links for v6

AngelHerraez: AngelHerraez moved page MediaWiki/Installation to MediaWiki/Installation/v5 without leaving a redirect: archving doc for v5; v6 will now be default installation instructions

2025-01-15T17:45:37Z

AngelHerraez moved page MediaWiki/Installation to MediaWiki/Installation/v5 without leaving a redirect: archving doc for v5; v6 will now be default installation instructions

AngelHerraez: /* Configuring recognition of molecular files */

2024-05-11T15:27:58Z

‎Configuring recognition of molecular files

AngelHerraez: Update of Managing molecular structure files with current MW info

2024-05-11T11:27:15Z

Update of Managing molecular structure files with current MW info

AngelHerraez: /* Authorizing uploads */

2024-05-11T10:44:46Z

‎Authorizing uploads

AngelHerraez at 09:15, 4 May 2024

2024-05-04T09:15:06Z

AngelHerraez at 10:47, 3 May 2024

2024-05-03T10:47:56Z

AngelHerraez: link to using the extension

2024-05-03T10:46:13Z

link to using the extension

AngelHerraez: /* File icons */

2024-05-03T10:03:06Z

‎File icons

← Older revision		Revision as of 19:13, 15 January 2025
Line 1:		Line 1:
−	= Installation of the Jmol (JSmol) Extension for Mediawiki, v6 =	+	= Installation of the Jmol (JSmol) Extension for Mediawiki, v5 =

	:<span style="color:white;font-weight:bold;background:#008F00;padding:0 1ex;">Admin</span> ''All this must be done by the wiki administrator.''		:<span style="color:white;font-weight:bold;background:#008F00;padding:0 1ex;">Admin</span> ''All this must be done by the wiki administrator.''

@@ Line 1: / Line 1: @@
-= Installation of the Jmol (JSmol) Extension for Mediawiki =
+= Installation of the Jmol (JSmol) Extension for Mediawiki, v6 =
 :<span style="color:white;font-weight:bold;background:#008F00;padding:0 1ex;">Admin</span> ''All this must be done by the wiki administrator.''
@@ Line 7: / Line 7: @@
 [[File:Jmol_Extension_5_folders_setup_3.png|frame|right|arrangement of folders and files of the Jmol Extension]]
 '''Note:''' '''Version 5''' of the Jmol Extension has been tested against MediaWiki 1.32. There are significant changes in MediaWiki, so this procedure will not work with older versions. It is not compatible either with newest versions of MediaWiki.
-''There is work in progress for a v.6 of the extension to be compatible with MediaWIki 1.41''
+There is [[MediaWiki/Extension|'''version 6''']] of the extension, compatible with MediaWiki 1.39, 14.1 and 1.43
 == To install the Jmol extension using Jmol 14 ==
@@ Line 128: / Line 128: @@
 = See also =
-[[MediaWiki/Extension|How to use the Extension]]
+[[MediaWiki/ExtensionV5|How to use the Extension v5]]

@@ Line 73: / Line 73: @@
 Recent versions of MediwWiki (e.g. 1.41) already include by default recognition of MIME type of {{file|.pdb}}, {{file|.xyz}} and {{file|.mol}} files (as well as other MDL-MOLfile formats like 'sdf', 'rxn', 'rd' and 'rg' extensions).
-When that is not enough, having a more precise MIME type detection is better, especially for the Media Handler.
+Near the end of your {{file|LocalSettings.php}} file, add these lines:
-For molecular file formats based on XML, the MIME type detection can be enhanced using {{MWmanual|$wgXMLMimeTypes}} , which allows the mapping between the root element of the file and the MIME type.
+<pre>$wgHooks['MimeMagicImproveFromExtension'][] = static function ( $mimeAnalyzer, $ext, &$mime ) {
-For example, for enhancing detection for [[:en:Chemical Markup Language|CML files]] {{File|*.cml}}, you can add the following lines in your {{file|LocalSettings.php}} file:
+  if     ( $ext == 'mol' ) { $mime = 'chemical/x-mdl-molfile'; }
 <pre>$wgXMLMimeTypes = array_merge( $wgXMLMimeTypes, array(
    'http://www.xml-cml.org/schema:cml'                => 'chemical/x-cml',
@@ Line 83: / Line 93: @@
    'http://www.xml-cml.org/schema/cml2/core:molecule' => 'chemical/x-cml' ) );
 </pre>
 By default, MediaWiki checks that the file extension matches the MIME type that has been detected.

@@ Line 51: / Line 51: @@
 == Managing molecular structure files ==
 === Authorizing uploads ===
-If you want to authorize users to upload files containing molecular data (for using the {{Tag|uploadedFileContents}} tag), you need to do the following:
+==== Web server PHP setup ====
-By default, MediaWiki authorizes the uploading of
+==== Wiki upload setup ====
-<!--
+If you want to authorize users to upload files containing molecular data (for using the {{Tag|uploadedFileContents}} subtag), you need to do the following:
-files whose name ends with a limited number of extensions. For example, if you want to authorize uploading {{File|*.cml}} files, add <tt>$wgFileExtensions[] = 'cml';</tt> in {{File|LocalSettings.php}}.
--->
+By default, MediaWiki authorizes the uploading of a very limited set of file types, based on file extensions and MIME types (see {{MWmanual|Configuring_file_uploads}}). By default, uploading molecular files is not authorized, so the configuration must be modified to take advantage of all the Jmol extension features.
 You can check what file extensions are authorized in the [[Special:Upload]] page.
 First, you need to authorize new file extensions being uploaded in the wiki, using {{MWmanual|$wgFileExtensions}}.
-For example, if you want to authorize uploading of [[:en:Chemical Markup Language|CML files]] {{File|*.cml}}, you can add the following line in your {{file|LocalSettings.php}} file:
+For example, add one or several of the following lines at the end of your {{file|LocalSettings.php}} file:
   $wgFileExtensions[] = 'cml';
-By default, the {{MWmanual|Mime_type_detection|MIME type detection}} configuration of MediaWiki only detects molecular files as basic  MIME types (<code>text/plain</code>, <code>application/xml</code>, …). Having a more precise MIME type detection is better, especially for the Media Handler.
+=== Configuring recognition of molecular files ===
 For molecular file formats based on XML, the MIME type detection can be enhanced using {{MWmanual|$wgXMLMimeTypes}} , which allows the mapping between the root element of the file and the MIME type.
 For example, for enhancing detection for [[:en:Chemical Markup Language|CML files]] {{File|*.cml}}, you can add the following lines in your {{file|LocalSettings.php}} file:
@@ Line 80: / Line 83: @@
    'http://www.xml-cml.org/schema/cml2/core:molecule' => 'chemical/x-cml' ) );
 </pre>
 By default, MediaWiki checks that the file extension matches the MIME type that has been detected.
-For this, MediaWiki uses the {{file|includes/mime.types}} file in MediaWiki installation.
+For this, MediaWiki uses {{file|includes/libs/mime/MimeMap.php}} in MediaWiki installation. In former MW versions, the file is {{file|includes/mime.types}}.
 File extensions for molecular models are probably missing from this file by default, so you need to modify it.
-For example, {{file|*.cml}} can be detected as <code>chemical/x-cml</code> or <code>application/xml</code> (depending on your {{MWmanual|Mime_type_detection|MIME type detection}} configuration), so you need to make the following additions to {{file|includes/mime.types}}:
+For example, {{file|*.cml}} might be detected as <code>chemical/x-cml</code> or <code>application/xml</code> (depending on your {{MWmanual|Mime_type_detection|MIME type detection}} configuration), so you need to make the following additions to {{file|includes/libs/mime/MimeMap.php}} or {{file|includes/mime.types}}:
   application/xml xml xsl xsd '''cml'''
   '''chemical/x-cml cml'''
 === File icons ===

@@ Line 72: / Line 72: @@
 By default, the {{MWmanual|Mime_type_detection|MIME type detection}} configuration of MediaWiki only detects molecular files as basic  MIME types (<code>text/plain</code>, <code>application/xml</code>, …). Having a more precise MIME type detection is better, especially for the Media Handler.
-For molecular file formats based on XML, the MIME type detection can be enhanced using {{MWmanual|$wgXMLMimeTypes}} which allows the mapping between the root element of the file and the MIME type.
+For molecular file formats based on XML, the MIME type detection can be enhanced using {{MWmanual|$wgXMLMimeTypes}} , which allows the mapping between the root element of the file and the MIME type.
 For example, for enhancing detection for [[:en:Chemical Markup Language|CML files]] {{File|*.cml}}, you can add the following lines in your {{file|LocalSettings.php}} file:
 <pre>$wgXMLMimeTypes = array_merge( $wgXMLMimeTypes, array(

← Older revision	Revision as of 17:45, 15 January 2025
(No difference)

@@ Line 6: / Line 6: @@
 [[File:Jmol_Extension_5_folders_setup_3.png|frame|right|arrangement of folders and files of the Jmol Extension]]
-'''Note:''' Version 5 of the Jmol Extension has been tested against MediaWiki 1.32. There are significant changes in MediaWiki, so this procedure will not work with older versions. It is not compatible either with newest versions of MediaWiki.
+'''Note:''' '''Version 5''' of the Jmol Extension has been tested against MediaWiki 1.32. There are significant changes in MediaWiki, so this procedure will not work with older versions. It is not compatible either with newest versions of MediaWiki.
 == To install the Jmol extension using Jmol 14 ==
@@ Line 93: / Line 93: @@
 == Installation of older versions ==
-Version 4 of the Jmol Extension is compatible with MediaWiki 1.16; [https://www.mediawiki.org/w/index.php?title=Extension:Jmol&oldid=2497254 installation instructions].
+'''Version 4''' of the Jmol Extension is compatible with MediaWiki 1.16; [https://www.mediawiki.org/w/index.php?title=Extension:Jmol&oldid=2497254 installation instructions].
-The Jmol Extension below v. 3.3 uses another extension, [[mw:Extension:StubManager|Stub Manager]], so you first need to install it.
+The Jmol Extension below '''version 3.3''' uses another extension, [[mw:Extension:StubManager|Stub Manager]], so you first need to install it.
 == Deprecated ==

← Older revision		Revision as of 10:46, 3 May 2024
Line 101:		Line 101:

	That page has been removed since the Jmol Extension is not compatible with recent versions of MediaWiki.		That page has been removed since the Jmol Extension is not compatible with recent versions of MediaWiki.
		+
		+	= See also =
		+	[[MediaWiki/Extension\|How to use the Extension]]

@@ Line 89: / Line 89: @@
 === File icons ===
-[[File:Fileicon_Chemical.png|thumb|Example icon]]Now that uploading new file extensions has been authorized, you can do a final modification so that molecular files are shown with a specific icon in categories (see examples in [[:Category:XYZ_file]]).
+[[File:Fileicon_Chemical.png|50px|right|Example icon]]Now that uploading new file extensions has been authorized, you can do a final modification so that molecular files are shown with a specific icon in categories (see examples in [[:Category:XYZ_file]]).
 You can add an icon in the {{folder|skins/common/images/icons}} folder for each extension of molecular files (such as {{file|fileicon-cml.png}}).