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Difference between revisions of "User talk:Harry Brumer"

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== To-do list ==
 
== To-do list ==
−
* Fix "content is available under..." statement on displayed '''and printed''' pages.
+
* Contribution credits?
−
* Write pages!
+
** http://www.mediawiki.org/wiki/Extension:ContributionCredits
−
* Static pages? http://en.wikipedia.org/wiki/Wikipedia:Database_download#Static_HTML_tree_dumps_for_mirroring_or_CD_distribution
+
 
−
* Page-level access control? http://www.mediawiki.org/wiki/Category:Page_Access_Control_Extensions
+
* Write a history/timeline page
 +
 
 +
* NewUserMessage could be good
 +
** http://www.mediawiki.org/wiki/Extension:NewUserMessage
 +
 
 +
* Static pages?
 +
** http://www.mediawiki.org/wiki/Extension:DumpHTML
 +
** http://en.wikipedia.org/wiki/Wikipedia:Database_download#Static_HTML_tree_dumps_for_mirroring_or_CD_distribution
 +
* RSS feeds for all pages?
 +
** http://jimbojw.com/wiki/index.php?title=WikiArticleFeeds_Extension
 +
 
 +
* Should use MultiBoilerplate at some point!
 +
** http://www.mediawiki.org/wiki/Extension:MultiBoilerplate
 +
**http://www.mediawiki.org/wiki/Manual:Creating_pages_with_preloaded_text
 +
 
 +
* Add LookupUser extension, maybe UserSnoop
 +
** http://www.mediawiki.org/wiki/Extension:LookupUser
 +
** http://www.mediawiki.org/wiki/Extension:UserSnoop
 +
 
 +
* Add ContactPage extension (consider captch implementation)
 +
** http://www.mediawiki.org/wiki/Extension:ContactPage
 +
 
 +
* Performance tuning
 +
** http://www.mediawiki.org/wiki/Manual:Performance_tuning
 +
 
 +
* User Contact Links looks slick.
 +
** http://www.mediawiki.org/wiki/Extension:User_Contact_Links
 +
 
 +
* Who Is Watching pages?
 +
** http://www.mediawiki.org/wiki/Extension:WhoIsWatchingTabbed
 +
** see also also related extensions on that page.
 +
 
 +
=== Substrate specificity test ===
 +
<gallery widths=150px heights=100px perrow=5 caption="Substrate specificites in GHxx (click images for large versions)">
 +
File:Glcase.png|beta-glucosidase
 +
File:Galase.png|beta-galactosidase
 +
</gallery>
 +
 
 +
 
 +
 
 +
<gallery widths=300px heights=100px perrow=5 caption="Substrate specificites in GHxx (click images for large versions)">
 +
File:EGase.png|endo-beta(1,4)-glucanase
 +
File:CBH.png|cellobiohydrolase
 +
</gallery>
 +
 
 +
== User admin ==
 +
=== Direct link to account creation page ===
 +
http://www.cazypedia.org/index.php?title=Special:UserLogin&type=signup
 +
 
 +
=== Extensions which are installed ===
 +
See also: [[Special:Version]] and  [[Special:Specialpages]]
 +
* ''Note: The list of users, blocking users, renaming users, and user rights management can all be accessed at [[Special:Specialpages]].''
 +
; Rename user: http://www.mediawiki.org/wiki/Extension:Renameuser
 +
; reCAPTCHA - anti spam: http://www.mediawiki.org/wiki/Extension:ReCAPTCHA
 +
; New user log: ''Accessible at [[Special:Log/newusers]]'' http://www.mediawiki.org/wiki/Newuserlog
 +
; Mass emailer: [[Special:MassEmail]]
 +
 
 +
=== Other useful user admin stuff ===
 +
; Prevent access, especially ACCOUNT CREATION BY SYSOPS ONLY: http://www.mediawiki.org/wiki/Manual:Preventing_access
 +
; Add confirm account extension instead?: http://www.mediawiki.org/wiki/Extension:ConfirmAccount
 +
 
 +
 
 +
=== Optional admin stuff, maybe for future implementation ===
 +
; Page-level access control?: http://www.mediawiki.org/wiki/Category:Page_Access_Control_Extensions
 
; New user email notification: http://www.mediawiki.org/wiki/Extension:New_User_Email_Notification
 
; New user email notification: http://www.mediawiki.org/wiki/Extension:New_User_Email_Notification
 +
; Password reset extension: http://www.mediawiki.org/wiki/Extension:Password_Reset
  
−
== Where the frick do I find... ==
+
== Where do I find... ==
 
; The navigation sidebar settings: [[MediaWiki:Sidebar]]
 
; The navigation sidebar settings: [[MediaWiki:Sidebar]]
 
; The boilerplate text automatically inserted by Preloader.php upon new page creation in the main namespace: [[Template:Boilerplate]]
 
; The boilerplate text automatically inserted by Preloader.php upon new page creation in the main namespace: [[Template:Boilerplate]]
 
; MediaWiki sysadmin Hub: http://www.mediawiki.org/wiki/Sysadmin_hub
 
; MediaWiki sysadmin Hub: http://www.mediawiki.org/wiki/Sysadmin_hub
 +
; Redirect code: <nowiki>#redirect [[Glycoside Hydrolase Family 16]]</nowiki>
  
 
== Some useful configuration pages  ==
 
== Some useful configuration pages  ==
Line 20: Line 85:
  
 
== Some useful extensions ==
 
== Some useful extensions ==
−
=== Biolerplate extension - might be useful for creating new page templates ===
+
=== Boilerplate extension - might be useful for creating new page templates ===
 
http://www.mediawiki.org/wiki/Extension:Boilerplate
 
http://www.mediawiki.org/wiki/Extension:Boilerplate
 
http://www.mediawiki.org/wiki/Extension:Preloader
 
http://www.mediawiki.org/wiki/Extension:Preloader
  
−
=== reCAPTCHA - anti spam ===
+
== Referencing extensions ==
−
http://www.mediawiki.org/wiki/Extension:ReCAPTCHA
+
 
 +
http://www.mediawiki.org/wiki/Category:Referencing_extensions
 +
 
 +
=== Biblio ===
 +
http://www.mediawiki.org/wiki/Extension:Biblio
 +
http://openwetware.org/wiki/Wikiomics:Biblio
 +
 
 +
=== Extension:Pubmed ===
 +
http://www.mediawiki.org/wiki/Extension:Pubmed
 +
 
 +
=== Extension:PubmedParser ===
 +
http://www.mediawiki.org/wiki/Extension:PubmedParser
 +
=== BiblioPlus ===
  
−
== Handle refs. with Biblio: ==
+
* https://www.mediawiki.org/wiki/Extension:BiblioPlus
−
http://wikiomics.org/wiki/Biblio
+
* PubMed API: https://www.ncbi.nlm.nih.gov/books/NBK25497/
 +
* Open Library Books API: https://openlibrary.org/dev/docs/api/books
  
 
== some templates from wikipedia ==
 
== some templates from wikipedia ==
 
http://en.wikipedia.org/wiki/Wikipedia:Template_messages
 
http://en.wikipedia.org/wiki/Wikipedia:Template_messages
 +
 +
one thing that is semi ugly is that your login name appears at the top of your page or in the list of contributors (for instance User:HBrumer3 or User:Bernie); wouldn't it be nicer if the full real name of people would appear just like on the Board of Curators' page with Harry Brumer or Bernard Henrissat ?
 +
 +
== Useful icons gallery ==
 +
http://commons.wikimedia.org/wiki/User:Ipatrol/Galleries/Icons
 +
 +
http://commons.wikimedia.org/wiki/User:Rocket000/Useful_icon_gallery
 +
 +
== Log ==
 +
 +
This section is a little Mediawiki maintenance log, which might become it's own page some day.
 +
 +
Started 02 September 2009.
 +
 +
=== UserContactLinks extended syntax extension ===
 +
* http://www.mediawiki.org/wiki/Extension:User_Contact_Links
 +
* Allows replacement of "<nowiki>[[:User:username|full name]]</nowiki>" with "''(3 tildes)''User Name''(3 tildes)''", where User Name can be:
 +
** wiki username
 +
** user full name (first space last)
 +
** last name of the user
 +
** partial match of any part of user full name
 +
* Had to slightly edit both PHP files to break-up ''(3 tildes)''User Name''(3 tildes)'' to "^^^user^^ ^" in description; this was resulting in "incorrect user" being shown on [[Special:Version]].
 +
 +
[[User:Harry Brumer|Harry Brumer]] 07:59, 2 September 2009 (UTC)
 +
 +
=== Implemented ContactPage extension ===
 +
* http://www.mediawiki.org/wiki/Extension:ContactPage
 +
* Gives world-accessible contact form: [[Special:Contact]]
 +
* Took some tweaking to get it to work:
 +
** Line 125 in SpecialContact.php (<nowiki>$captcha = ConfirmEditHooks::getInstance();</nowiki>) broke Mediawiki
 +
** Upgrading to ConfirmEdit-MW1.15-r50221 broke reCaptcha, e.g. on [http://www.cazypedia.org/index.php?title=Special:UserLogin&type=signup user signup page].
 +
** '''Fixed by commenting out offending Line 125'''
 +
*** All seems OK
 +
*** reCaptcha works on all pages, including [[Special:Contact]] (must not be logged in as sysop to see it) and [http://www.cazypedia.org/index.php?title=Special:UserLogin&type=signup user signup page]
 +
* Also hacked ConfirmEdit.php to put "contactpage" captcha trigger there, instead of in LocalSettings.php (left a comment in the latter to that effect).
 +
 +
[[User:Harry Brumer|Harry Brumer]] 15:43, 2 September 2009 (UTC)
 +
 +
=== Playing around with image thumbnail settings ===
 +
* see http://www.mediawiki.org/wiki/Image_thumbnailing
 +
* $wgUseImageMagick turned off in LocalSettings.php
 +
** Was generating errors on [[Special:NewFiles]] (ImageMagick not installed...)
 +
* Not clear if $wgUseImageResize should be used or not in MW 1.15
 +
** Unclear info at  http://www.mediawiki.org/wiki/Manual:$wgUseImageResize
 +
** Now uncommented  in LocalSettings.php, maybe some effect with .gif (see [[GH11]]).
 +
 +
[[User:Harry Brumer|Harry Brumer]] 14:12, 7 September 2009 (UTC)
 +
 +
=== Implemented Extension:Cite/Special:Cite.php ===
 +
* Generates full citation information for each page via a toolbox link
 +
* see http://www.mediawiki.org/wiki/Extension:Cite/Special:Cite.php
 +
** [[Mediawiki:Cite text]] created from cite_text file in extension directory (contains citation formats & layout)
 +
 +
[[User:Harry Brumer|Harry Brumer]] 13:12, 5 November 2009 (UTC)
 +
 +
* "Date retrieved" code doesn't seem to be working right.  Tried to implement a solution Wikipedia is running using the ParserFunction extension and the time function, but ParserFunction seems to break the wiki.  Also, had to disable MassEmailer due to some weird conflict that generated an error trail when saving [[Mediawiki:Cite text]].
 +
 +
[[User:Harry Brumer|Harry Brumer]] 15:13, 5 November 2009 (UTC)
 +
 +
==== New version (r50579) of Extension:ParserFunctions added ====
 +
* Fixed earlier problem with ParserFunctions breaking the wiki
 +
* Allow use of '''time''' function in [[Mediawiki:Cite text]] to give the current time in the "Date retrieved" line.
 +
 +
[[User:Harry Brumer|Harry Brumer]] 09:39, 6 November 2009 (UTC)
 +
 +
=== Pages in Category test ===
 +
* Might be something for MainPage, although claimed to be "expensive": http://www.mediawiki.org/wiki/Help:Magic_words
 +
* See also http://www.mediawiki.org/wiki/Manual:$wgExpensiveParserFunctionLimit
 +
** Now containing [[:Category:Glycoside Hydrolase Families|{{PAGESINCATEGORY:Glycoside Hydrolase Families}} GH family pages]] and [[:Category:Definitions and explanations|{{PAGESINCATEGORY:Definitions and explanations}} lexicon pages]].
 +
 +
[[User:Harry Brumer|Harry Brumer]] 10:35, 8 November 2009 (UTC)
 +
 +
=== Stopped implementing Extension:EditUser ===
 +
* http://www.mediawiki.org/wiki/Extension:EditUser
 +
** On ice for the moment.
 +
** ChangePassword mainentance script will probably do what I need for now. http://www.mediawiki.org/wiki/Manual:ChangePassword.php
 +
 +
[[User:Harry Brumer|Harry Brumer]] 13:29, 8 November 2009 (UTC)
 +
 +
=== Implemented Extension:LookupUser ===
 +
* http://www.mediawiki.org/wiki/Extension:LookupUser
 +
* Gives SpecialPage [[Special:LookupUser]] showing user prefs., including email address.
 +
* Currently accessible only to Bureaucrat group only (LocalSettings)
 +
 +
[[User:Harry Brumer|Harry Brumer]] 13:48, 8 November 2009 (UTC)
 +
 +
=== Implemented [[:Template:Smallcaps]] ===
 +
* Wraps some markup for simple implementation of {{Smallcaps|small caps}}, e.g. for use in {{Smallcaps|d}}/{{Smallcaps|l}} sugar nomenclature.
 +
* '''NOTE''' ''(from the [http://en.wikipedia.org/wiki/Template:Smallcaps/doc Smallcaps template doc page)'':
 +
<blockquote>
 +
Your source text is not altered in the output, only the way it is displayed on the screen: a copy-paste of the text will give the small caps sections in their original form; similarly, an older or non-CSS browser will only display the original text on screen. This can be seen as a problem, solved with (the sc template).
 +
 +
; Code    : <code><nowiki>{{Smallcaps|Your Text in 4004 bc}}</nowiki></code>
 +
; Displayed: {{Smallcaps|Your Text in 4004 bc}}
 +
; Pasted  : Your Text in 4004 bc
 +
</blockquote>
 +
* So, the code needs to look like this: <code><nowiki>{{Smallcaps|d}}</nowiki></code>, to get {{Smallcaps|d}}.  <code><nowiki>{{Smallcaps|D}}</nowiki></code> gives {{Smallcaps|D}}.
 +
 +
[[User:Harry Brumer|Harry Brumer]] 16:27, 6 January 2010 (UTC)
 +
 +
=== Tested Extension:DynamicPageList (a.k.a. Intersection) ===
 +
* Allows showing intersections of Categories
 +
* http://en.wikinews.org/wiki/Wikinews:DynamicPageList
 +
** Worked OK but could only give simple linear lists.
 +
** Was difficult to figure out how to sort alphabetically given limited documentation, had to read the code to find the "categorysortkey" option.
 +
** e.g., this sort of worked:
 +
<pre>
 +
<DynamicPageList>
 +
category=Glycoside Hydrolase Families
 +
category=Curator approved
 +
ordermethod=categorysortkey
 +
order=ascending
 +
mode=none
 +
</DynamicPageList>
 +
</pre>
 +
* However, not really pretty. '''Extension disabled.'''
 +
* Might use '''DynamicPageList2''':  http://www.mediawiki.org/wiki/Extension:DynamicPageList_(third-party)
 +
 +
[[User:Harry Brumer|Harry Brumer]] 12:00, 23 January 2010 (UTC)
 +
 +
=== Implementing Extension:DynamicPageList2 ===
 +
* Allows showing intersections of Categories, plus many page analysis features.
 +
* Essentially supercedes Extension:DynamicPageList
 +
* http://www.mediawiki.org/wiki/Extension:DynamicPageList_(third-party)
 +
* http://semeb.com/dpldemo/index.php?title=Extension_DPL
 +
 +
==== Examples ====
 +
----
 +
* Pages in categories ''Glycoside Hydrolase Families'' and ''Curator  approved'', sorted by title, formatted as a normal category page.
 +
 +
<pre>
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|mode=category
 +
|ordermethod=sortkey
 +
|allowcachedresults=true
 +
}}
 +
</pre>
 +
 +
''Had to deleted live code after testing here, output was messing up table of contents  above: Each "G" in the list was getting it's own subheading TOC entry.''
 +
 +
----
 +
* Pages in  categories ''Glycoside Hydrolase Families'' and ''Curator approved'', sorted by title, formatted "inline."
 +
 +
<pre>
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
 +
|mode=inline
 +
|ordermethod=sortkey
 +
|order=descending
 +
|allowcachedresults=yes+warn
 +
}}
 +
</pre>
 +
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
 +
|mode=inline
 +
|ordermethod=sortkey
 +
|order=descending
 +
|allowcachedresults=yes+warn
 +
}}
 +
 +
----
 +
* Pages in categories ''Glycoside Hydrolase Families'' and ''Curator  approved'', in a sortable table. ''Note!: Needs the dummy '''include''' line, or no output is produced.''
 +
 +
<pre>
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
 +
|ordermethod=sortkey
 +
|include=-
 +
|table=class=sortable,GH Families
 +
|allowcachedresults=true
 +
}}
 +
</pre>
 +
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
 +
|ordermethod=sortkey
 +
|include=-
 +
|table=class=sortable,GH  Families
 +
|allowcachedresults=true
 +
}}
 +
 +
[[User:Harry Brumer|Harry Brumer]] 19:57, 23 January 2010 (UTC)
 +
 +
----
 +
* Just display number of pages in two categories without a page list.
 +
 +
<pre>
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% [[:Category:Curator approved]] GH pages.\n
 +
|mode=userformat
 +
}}
 +
</pre>
 +
 +
{{#dpl:
 +
|category=Glycoside Hydrolase Families
 +
|category=Curator approved
 +
|resultsheader=\nThere are %TOTALPAGES% [[:Category:Curator approved|Curator Approved]] GH pages.\n
 +
|mode=userformat
 +
}}
 +
 +
[[User:Harry Brumer|Harry Brumer]] 14:01, 12 February 2010 (UTC)
 +
 +
 +
=== Biblio character encoding problem ===
 +
A couple of PMIDs seem to not work with the current Biblio.php script hack to switch the character encoding into UTF-8:
 +
* pmid=16533067 on the [[GH84]] page (see History, June 30, 2010)
 +
* Markovic-Housley2000 pmid=11080624 on the [[Syn/anti lateral protonation]] page (see History, June 30, 2010)
 +
 +
[[User:Harry Brumer|Harry Brumer]] 12:24, 29 July 2010 (UTC)
 +
 +
 +
=== Upgraded to MW1.16.0 ===
 +
* Most everything works fine
 +
* Upgraded Extension:ParserFunctions
 +
** Extension:StringFunctions now folded into Extension:ParserFunctions, so required changes made in LocalSettings
 +
 +
==== Broken ====
 +
===== Extension:WhoIsWatchingTabbed =====
 +
Extension:WhoIsWatchingTabbed does not render the tab with the Vector skin
 +
* ...but can still be called via the URL using "action=watching"
 +
* e.g. http://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Families&action=watching
 +
 +
===== Extension:DynamicPageList2 =====
 +
Extension:DynamicPageList2 does not seem to work properly...
 +
* Renders HTML tags in page lists from Categories
 +
** See http://www.mediawiki.org/wiki/Extension_talk:DynamicPageList_%28third-party%29#MediaWiki_1.17alpha_and_bug_22675
 +
** also http://www.mediawiki.org/wiki/Special:Code/MediaWiki/68812
 +
* Use of $wgRawHtml = true with the current trunk version, DynamicPageList-trunk-r70760.tar.gz, fixes problem, '''but breaks Biblio''' due to $wgRawHtml = true (if not set to true, DPL2 is still broken)
 +
* Counting total pages in a union of two categories seems not to work quite right.
 +
 +
[[User:Harry Brumer|Harry Brumer]] 11:54, 11 August 2010 (CEST)
 +
 +
Testing [http://www.mediawiki.org/wiki/Extension:Intersection Extension:Intersection] again...
 +
 +
These both worked, but layout not quite as nice:
 +
 +
* Simple bulleted linear list
 +
<pre>
 +
<DynamicPageList>
 +
category=Glycoside Hydrolase Families
 +
category=Curator approved
 +
ordermethod=categorysortkey
 +
order=ascending
 +
mode=unordered
 +
</DynamicPageList>
 +
</pre>
 +
 +
* Forcing 3 columns for 60 pages
 +
 +
<pre>
 +
<table>
 +
<tr><th colspan="3"> recent articles </th></tr>
 +
<tr><td>
 +
 +
<DynamicPageList>
 +
category=Glycoside Hydrolase Families
 +
category=Curator approved
 +
ordermethod=categorysortkey
 +
order=ascending
 +
count=20
 +
</DynamicPageList>
 +
</td>
 +
<td>
 +
<DynamicPageList>
 +
category=Glycoside Hydrolase Families
 +
category=Curator approved
 +
ordermethod=categorysortkey
 +
order=ascending
 +
offset=20
 +
count=20
 +
</DynamicPageList>
 +
</td>
 +
<td>
 +
 +
<DynamicPageList>
 +
category=Glycoside Hydrolase Families
 +
category=Curator approved
 +
ordermethod=categorysortkey
 +
order=ascending
 +
offset=40
 +
count=20
 +
</DynamicPageList>
 +
</td></tr></table>
 +
 +
</pre>
 +
 +
DPL2 and Intersection can't be run at the same time; DPL2 recognizes <nowiki><DynamicPageList></nowiki> tags and tries to work on the code, with syntax errors.
 +
 +
[[User:Harry Brumer|Harry Brumer]] 12:31, 11 August 2010 (CEST)

Latest revision as of 16:33, 21 January 2022

To-do list

  • Write a history/timeline page

Substrate specificity test

  • Substrate specificites in GHxx (click images for large versions)

  • beta-glucosidase

  • beta-galactosidase


  • Substrate specificites in GHxx (click images for large versions)

  • endo-beta(1,4)-glucanase

  • cellobiohydrolase

User admin

Direct link to account creation page

http://www.cazypedia.org/index.php?title=Special:UserLogin&type=signup

Extensions which are installed

See also: Special:Version and Special:Specialpages

  • Note: The list of users, blocking users, renaming users, and user rights management can all be accessed at Special:Specialpages.
Rename user
http://www.mediawiki.org/wiki/Extension:Renameuser
reCAPTCHA - anti spam
http://www.mediawiki.org/wiki/Extension:ReCAPTCHA
New user log
Accessible at Special:Log/newusers http://www.mediawiki.org/wiki/Newuserlog
Mass emailer
Special:MassEmail

Other useful user admin stuff

Prevent access, especially ACCOUNT CREATION BY SYSOPS ONLY
http://www.mediawiki.org/wiki/Manual:Preventing_access
Add confirm account extension instead?
http://www.mediawiki.org/wiki/Extension:ConfirmAccount


Optional admin stuff, maybe for future implementation

Page-level access control?
http://www.mediawiki.org/wiki/Category:Page_Access_Control_Extensions
New user email notification
http://www.mediawiki.org/wiki/Extension:New_User_Email_Notification
Password reset extension
http://www.mediawiki.org/wiki/Extension:Password_Reset

Where do I find...

The navigation sidebar settings
MediaWiki:Sidebar
The boilerplate text automatically inserted by Preloader.php upon new page creation in the main namespace
Template:Boilerplate
MediaWiki sysadmin Hub
http://www.mediawiki.org/wiki/Sysadmin_hub
Redirect code
#redirect [[Glycoside Hydrolase Family 16]]

Some useful configuration pages

Sitenotice - for adding info to every page

MediaWiki:Sitenotice

Sitesubtitle - Edited, not sure of the effect...

MediaWiki:Sitesubtitle


Some useful extensions

Boilerplate extension - might be useful for creating new page templates

http://www.mediawiki.org/wiki/Extension:Boilerplate http://www.mediawiki.org/wiki/Extension:Preloader

Referencing extensions

http://www.mediawiki.org/wiki/Category:Referencing_extensions

Biblio

http://www.mediawiki.org/wiki/Extension:Biblio http://openwetware.org/wiki/Wikiomics:Biblio

Extension:Pubmed

http://www.mediawiki.org/wiki/Extension:Pubmed

Extension:PubmedParser

http://www.mediawiki.org/wiki/Extension:PubmedParser

BiblioPlus

some templates from wikipedia

http://en.wikipedia.org/wiki/Wikipedia:Template_messages

one thing that is semi ugly is that your login name appears at the top of your page or in the list of contributors (for instance User:HBrumer3 or User:Bernie); wouldn't it be nicer if the full real name of people would appear just like on the Board of Curators' page with Harry Brumer or Bernard Henrissat ?

Useful icons gallery

http://commons.wikimedia.org/wiki/User:Ipatrol/Galleries/Icons

http://commons.wikimedia.org/wiki/User:Rocket000/Useful_icon_gallery

Log

This section is a little Mediawiki maintenance log, which might become it's own page some day.

Started 02 September 2009.

UserContactLinks extended syntax extension

  • http://www.mediawiki.org/wiki/Extension:User_Contact_Links
  • Allows replacement of "[[:User:username|full name]]" with "(3 tildes)User Name(3 tildes)", where User Name can be:
    • wiki username
    • user full name (first space last)
    • last name of the user
    • partial match of any part of user full name
  • Had to slightly edit both PHP files to break-up (3 tildes)User Name(3 tildes) to "^^^user^^ ^" in description; this was resulting in "incorrect user" being shown on Special:Version.

Harry Brumer 07:59, 2 September 2009 (UTC)

Implemented ContactPage extension

  • http://www.mediawiki.org/wiki/Extension:ContactPage
  • Gives world-accessible contact form: Special:Contact
  • Took some tweaking to get it to work:
    • Line 125 in SpecialContact.php ($captcha = ConfirmEditHooks::getInstance();) broke Mediawiki
    • Upgrading to ConfirmEdit-MW1.15-r50221 broke reCaptcha, e.g. on user signup page.
    • Fixed by commenting out offending Line 125
  • Also hacked ConfirmEdit.php to put "contactpage" captcha trigger there, instead of in LocalSettings.php (left a comment in the latter to that effect).

Harry Brumer 15:43, 2 September 2009 (UTC)

Playing around with image thumbnail settings

Harry Brumer 14:12, 7 September 2009 (UTC)

Implemented Extension:Cite/Special:Cite.php

Harry Brumer 13:12, 5 November 2009 (UTC)

  • "Date retrieved" code doesn't seem to be working right. Tried to implement a solution Wikipedia is running using the ParserFunction extension and the time function, but ParserFunction seems to break the wiki. Also, had to disable MassEmailer due to some weird conflict that generated an error trail when saving Mediawiki:Cite text.

Harry Brumer 15:13, 5 November 2009 (UTC)

New version (r50579) of Extension:ParserFunctions added

  • Fixed earlier problem with ParserFunctions breaking the wiki
  • Allow use of time function in Mediawiki:Cite text to give the current time in the "Date retrieved" line.

Harry Brumer 09:39, 6 November 2009 (UTC)

Pages in Category test

Harry Brumer 10:35, 8 November 2009 (UTC)

Stopped implementing Extension:EditUser

Harry Brumer 13:29, 8 November 2009 (UTC)

Implemented Extension:LookupUser

Harry Brumer 13:48, 8 November 2009 (UTC)

Implemented Template:Smallcaps

Your source text is not altered in the output, only the way it is displayed on the screen: a copy-paste of the text will give the small caps sections in their original form; similarly, an older or non-CSS browser will only display the original text on screen. This can be seen as a problem, solved with (the sc template).

Code
{{Smallcaps|Your Text in 4004 bc}}
Displayed
Your Text in 4004 bc
Pasted
Your Text in 4004 bc
  • So, the code needs to look like this: {{Smallcaps|d}}, to get d. {{Smallcaps|D}} gives D.

Harry Brumer 16:27, 6 January 2010 (UTC)

Tested Extension:DynamicPageList (a.k.a. Intersection)

  • Allows showing intersections of Categories
  • http://en.wikinews.org/wiki/Wikinews:DynamicPageList
    • Worked OK but could only give simple linear lists.
    • Was difficult to figure out how to sort alphabetically given limited documentation, had to read the code to find the "categorysortkey" option.
    • e.g., this sort of worked:
<DynamicPageList>
category=Glycoside Hydrolase Families
category=Curator approved
ordermethod=categorysortkey
order=ascending
mode=none
</DynamicPageList>

Harry Brumer 12:00, 23 January 2010 (UTC)

Implementing Extension:DynamicPageList2

Examples

  • Pages in categories Glycoside Hydrolase Families and Curator approved, sorted by title, formatted as a normal category page.
{{#dpl:
|category=Glycoside Hydrolase Families
|category=Curator approved
|mode=category
|ordermethod=sortkey
|allowcachedresults=true
}}

Had to deleted live code after testing here, output was messing up table of contents above: Each "G" in the list was getting it's own subheading TOC entry.

  • Pages in categories Glycoside Hydrolase Families and Curator approved, sorted by title, formatted "inline."
{{#dpl:
|category=Glycoside Hydrolase Families
|category=Curator approved
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
|mode=inline
|ordermethod=sortkey
|order=descending
|allowcachedresults=yes+warn
}}


There are 140 Curator Approved GH pages.

Glycoside Hydrolase Family 189 - Glycoside Hydrolase Family 188 - Glycoside Hydrolase Family 187 - Glycoside Hydrolase Family 186 - Glycoside Hydrolase Family 174 - Glycoside Hydrolase Family 173 - Glycoside Hydrolase Family 172 - Glycoside Hydrolase Family 168 - Glycoside Hydrolase Family 164 - Glycoside Hydrolase Family 162 - Glycoside Hydrolase Family 158 - Glycoside Hydrolase Family 155 - Glycoside Hydrolase Family 151 - Glycoside Hydrolase Family 147 - Glycoside Hydrolase Family 146 - Glycoside Hydrolase Family 145 - Glycoside Hydrolase Family 144 - Glycoside Hydrolase Family 141 - Glycoside Hydrolase Family 140 - Glycoside Hydrolase Family 139 - Glycoside Hydrolase Family 138 - Glycoside Hydrolase Family 137 - Glycoside Hydrolase Family 136 - Glycoside Hydrolase Family 135 - Glycoside Hydrolase Family 134 - Glycoside Hydrolase Family 131 - Glycoside Hydrolase Family 130 - Glycoside Hydrolase Family 129 - Glycoside Hydrolase Family 128 - Glycoside Hydrolase Family 127 - Glycoside Hydrolase Family 125 - Glycoside Hydrolase Family 124 - Glycoside Hydrolase Family 123 - Glycoside Hydrolase Family 121 - Glycoside Hydrolase Family 120 - Glycoside Hydrolase Family 119 - Glycoside Hydrolase Family 117 - Glycoside Hydrolase Family 116 - Glycoside Hydrolase Family 115 - Glycoside Hydrolase Family 114 - Glycoside Hydrolase Family 113 - Glycoside Hydrolase Family 112 - Glycoside Hydrolase Family 110 - Glycoside Hydrolase Family 109 - Glycoside Hydrolase Family 107 - Glycoside Hydrolase Family 106 - Glycoside Hydrolase Family 105 - Glycoside Hydrolase Family 104 - Glycoside Hydrolase Family 103 - Glycoside Hydrolase Family 102 - Glycoside Hydrolase Family 101 - Glycoside Hydrolase Family 99 - Glycoside Hydrolase Family 98 - Glycoside Hydrolase Family 97 - Glycoside Hydrolase Family 95 - Glycoside Hydrolase Family 94 - Glycoside Hydrolase Family 93 - Glycoside Hydrolase Family 92 - Glycoside Hydrolase Family 89 - Glycoside Hydrolase Family 88 - Glycoside Hydrolase Family 86 - Glycoside Hydrolase Family 85 - Glycoside Hydrolase Family 84 - Glycoside Hydrolase Family 82 - Glycoside Hydrolase Family 81 - Glycoside Hydrolase Family 80 - Glycoside Hydrolase Family 79 - Glycoside Hydrolase Family 78 - Glycoside Hydrolase Family 77 - Glycoside Hydrolase Family 76 - Glycoside Hydrolase Family 75 - Glycoside Hydrolase Family 74 - Glycoside Hydrolase Family 73 - Glycoside Hydrolase Family 72 - Glycoside Hydrolase Family 70 - Glycoside Hydrolase Family 69 - Glycoside Hydrolase Family 68 - Glycoside Hydrolase Family 67 - Glycoside Hydrolase Family 66 - Glycoside Hydrolase Family 65 - Glycoside Hydrolase Family 64 - Glycoside Hydrolase Family 63 - Glycoside Hydrolase Family 62 - Glycoside Hydrolase Family 61 - Glycoside Hydrolase Family 60 - Glycoside Hydrolase Family 58 - Glycoside Hydrolase Family 57 - Glycoside Hydrolase Family 55 - Glycoside Hydrolase Family 54 - Glycoside Hydrolase Family 53 - Glycoside Hydrolase Family 52 - Glycoside Hydrolase Family 51 - Glycoside Hydrolase Family 50 - Glycoside Hydrolase Family 49 - Glycoside Hydrolase Family 48 - Glycoside Hydrolase Family 47 - Glycoside Hydrolase Family 46 - Glycoside Hydrolase Family 45 - Glycoside Hydrolase Family 44 - Glycoside Hydrolase Family 43 - Glycoside Hydrolase Family 42 - Glycoside Hydrolase Family 41 - Glycoside Hydrolase Family 40 - Glycoside Hydrolase Family 39 - Glycoside Hydrolase Family 38 - Glycoside Hydrolase Family 37 - Glycoside Hydrolase Family 36 - Glycoside Hydrolase Family 35 - Glycoside Hydrolase Family 34 - Glycoside Hydrolase Family 33 - Glycoside Hydrolase Family 32 - Glycoside Hydrolase Family 31 - Glycoside Hydrolase Family 30 - Glycoside Hydrolase Family 29 - Glycoside Hydrolase Family 28 - Glycoside Hydrolase Family 27 - Glycoside Hydrolase Family 26 - Glycoside Hydrolase Family 25 - Glycoside Hydrolase Family 23 - Glycoside Hydrolase Family 22 - Glycoside Hydrolase Family 21 - Glycoside Hydrolase Family 20 - Glycoside Hydrolase Family 19 - Glycoside Hydrolase Family 18 - Glycoside Hydrolase Family 17 - Glycoside Hydrolase Family 16 - Glycoside Hydrolase Family 15 - Glycoside Hydrolase Family 13 - Glycoside Hydrolase Family 12 - Glycoside Hydrolase Family 11 - Glycoside Hydrolase Family 10 - Glycoside Hydrolase Family 9 - Glycoside Hydrolase Family 8 - Glycoside Hydrolase Family 7 - Glycoside Hydrolase Family 6 - Glycoside Hydrolase Family 5 - Glycoside Hydrolase Family 4 - Glycoside Hydrolase Family 3 - Glycoside Hydrolase Family 2 - Glycoside Hydrolase Family 1
  • Pages in categories Glycoside Hydrolase Families and Curator approved, in a sortable table. Note!: Needs the dummy include line, or no output is produced.
{{#dpl:
|category=Glycoside Hydrolase Families
|category=Curator approved
|resultsheader=\nThere are %TOTALPAGES% Curator Approved GH pages.\n
|ordermethod=sortkey
|include=-
|table=class=sortable,GH Families
|allowcachedresults=true
}}


There are 140 Curator Approved GH pages.

GH Families
Glycoside Hydrolase Family 1
Glycoside Hydrolase Family 2
Glycoside Hydrolase Family 3
Glycoside Hydrolase Family 4
Glycoside Hydrolase Family 5
Glycoside Hydrolase Family 6
Glycoside Hydrolase Family 7
Glycoside Hydrolase Family 8
Glycoside Hydrolase Family 9
Glycoside Hydrolase Family 10
Glycoside Hydrolase Family 11
Glycoside Hydrolase Family 12
Glycoside Hydrolase Family 13
Glycoside Hydrolase Family 15
Glycoside Hydrolase Family 16
Glycoside Hydrolase Family 17
Glycoside Hydrolase Family 18
Glycoside Hydrolase Family 19
Glycoside Hydrolase Family 20
Glycoside Hydrolase Family 21
Glycoside Hydrolase Family 22
Glycoside Hydrolase Family 23
Glycoside Hydrolase Family 25
Glycoside Hydrolase Family 26
Glycoside Hydrolase Family 27
Glycoside Hydrolase Family 28
Glycoside Hydrolase Family 29
Glycoside Hydrolase Family 30
Glycoside Hydrolase Family 31
Glycoside Hydrolase Family 32
Glycoside Hydrolase Family 33
Glycoside Hydrolase Family 34
Glycoside Hydrolase Family 35
Glycoside Hydrolase Family 36
Glycoside Hydrolase Family 37
Glycoside Hydrolase Family 38
Glycoside Hydrolase Family 39
Glycoside Hydrolase Family 40
Glycoside Hydrolase Family 41
Glycoside Hydrolase Family 42
Glycoside Hydrolase Family 43
Glycoside Hydrolase Family 44
Glycoside Hydrolase Family 45
Glycoside Hydrolase Family 46
Glycoside Hydrolase Family 47
Glycoside Hydrolase Family 48
Glycoside Hydrolase Family 49
Glycoside Hydrolase Family 50
Glycoside Hydrolase Family 51
Glycoside Hydrolase Family 52
Glycoside Hydrolase Family 53
Glycoside Hydrolase Family 54
Glycoside Hydrolase Family 55
Glycoside Hydrolase Family 57
Glycoside Hydrolase Family 58
Glycoside Hydrolase Family 60
Glycoside Hydrolase Family 61
Glycoside Hydrolase Family 62
Glycoside Hydrolase Family 63
Glycoside Hydrolase Family 64
Glycoside Hydrolase Family 65
Glycoside Hydrolase Family 66
Glycoside Hydrolase Family 67
Glycoside Hydrolase Family 68
Glycoside Hydrolase Family 69
Glycoside Hydrolase Family 70
Glycoside Hydrolase Family 72
Glycoside Hydrolase Family 73
Glycoside Hydrolase Family 74
Glycoside Hydrolase Family 75
Glycoside Hydrolase Family 76
Glycoside Hydrolase Family 77
Glycoside Hydrolase Family 78
Glycoside Hydrolase Family 79
Glycoside Hydrolase Family 80
Glycoside Hydrolase Family 81
Glycoside Hydrolase Family 82
Glycoside Hydrolase Family 84
Glycoside Hydrolase Family 85
Glycoside Hydrolase Family 86
Glycoside Hydrolase Family 88
Glycoside Hydrolase Family 89
Glycoside Hydrolase Family 92
Glycoside Hydrolase Family 93
Glycoside Hydrolase Family 94
Glycoside Hydrolase Family 95
Glycoside Hydrolase Family 97
Glycoside Hydrolase Family 98
Glycoside Hydrolase Family 99
Glycoside Hydrolase Family 101
Glycoside Hydrolase Family 102
Glycoside Hydrolase Family 103
Glycoside Hydrolase Family 104
Glycoside Hydrolase Family 105
Glycoside Hydrolase Family 106
Glycoside Hydrolase Family 107
Glycoside Hydrolase Family 109
Glycoside Hydrolase Family 110
Glycoside Hydrolase Family 112
Glycoside Hydrolase Family 113
Glycoside Hydrolase Family 114
Glycoside Hydrolase Family 115
Glycoside Hydrolase Family 116
Glycoside Hydrolase Family 117
Glycoside Hydrolase Family 119
Glycoside Hydrolase Family 120
Glycoside Hydrolase Family 121
Glycoside Hydrolase Family 123
Glycoside Hydrolase Family 124
Glycoside Hydrolase Family 125
Glycoside Hydrolase Family 127
Glycoside Hydrolase Family 128
Glycoside Hydrolase Family 129
Glycoside Hydrolase Family 130
Glycoside Hydrolase Family 131
Glycoside Hydrolase Family 134
Glycoside Hydrolase Family 135
Glycoside Hydrolase Family 136
Glycoside Hydrolase Family 137
Glycoside Hydrolase Family 138
Glycoside Hydrolase Family 139
Glycoside Hydrolase Family 140
Glycoside Hydrolase Family 141
Glycoside Hydrolase Family 144
Glycoside Hydrolase Family 145
Glycoside Hydrolase Family 146
Glycoside Hydrolase Family 147
Glycoside Hydrolase Family 151
Glycoside Hydrolase Family 155
Glycoside Hydrolase Family 158
Glycoside Hydrolase Family 162
Glycoside Hydrolase Family 164
Glycoside Hydrolase Family 168
Glycoside Hydrolase Family 172
Glycoside Hydrolase Family 173
Glycoside Hydrolase Family 174
Glycoside Hydrolase Family 186
Glycoside Hydrolase Family 187
Glycoside Hydrolase Family 188
Glycoside Hydrolase Family 189

Harry Brumer 19:57, 23 January 2010 (UTC)

  • Just display number of pages in two categories without a page list.
{{#dpl:
|category=Glycoside Hydrolase Families
|category=Curator approved
|resultsheader=\nThere are %TOTALPAGES% [[:Category:Curator approved]] GH pages.\n
|mode=userformat
}}


There are 140 Curator Approved GH pages.


Harry Brumer 14:01, 12 February 2010 (UTC)


Biblio character encoding problem

A couple of PMIDs seem to not work with the current Biblio.php script hack to switch the character encoding into UTF-8:

  • pmid=16533067 on the GH84 page (see History, June 30, 2010)
  • Markovic-Housley2000 pmid=11080624 on the Syn/anti lateral protonation page (see History, June 30, 2010)

Harry Brumer 12:24, 29 July 2010 (UTC)


Upgraded to MW1.16.0

  • Most everything works fine
  • Upgraded Extension:ParserFunctions
    • Extension:StringFunctions now folded into Extension:ParserFunctions, so required changes made in LocalSettings

Broken

Extension:WhoIsWatchingTabbed

Extension:WhoIsWatchingTabbed does not render the tab with the Vector skin

Extension:DynamicPageList2

Extension:DynamicPageList2 does not seem to work properly...

Harry Brumer 11:54, 11 August 2010 (CEST)

Testing Extension:Intersection again...

These both worked, but layout not quite as nice:

  • Simple bulleted linear list
<DynamicPageList>
category=Glycoside Hydrolase Families
category=Curator approved
ordermethod=categorysortkey
order=ascending
mode=unordered
</DynamicPageList>
  • Forcing 3 columns for 60 pages
<table>
<tr><th colspan="3"> recent articles </th></tr>
<tr><td>

<DynamicPageList>
category=Glycoside Hydrolase Families
category=Curator approved
ordermethod=categorysortkey
order=ascending
count=20
</DynamicPageList>
</td>
<td>
<DynamicPageList>
category=Glycoside Hydrolase Families
category=Curator approved
ordermethod=categorysortkey
order=ascending
offset=20
count=20
</DynamicPageList>
</td>
<td>

<DynamicPageList>
category=Glycoside Hydrolase Families
category=Curator approved
ordermethod=categorysortkey
order=ascending
offset=40
count=20
</DynamicPageList>
</td></tr></table>

DPL2 and Intersection can't be run at the same time; DPL2 recognizes <DynamicPageList> tags and tries to work on the code, with syntax errors.

Harry Brumer 12:31, 11 August 2010 (CEST)

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