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Difference between revisions of "User talk:Harry Brumer"
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== Referencing extensions == | == Referencing extensions == | ||
| + | |||
http://www.mediawiki.org/wiki/Category:Referencing_extensions | http://www.mediawiki.org/wiki/Category:Referencing_extensions | ||
| Line 101: | Line 102: | ||
=== Extension:PubmedParser === | === Extension:PubmedParser === | ||
http://www.mediawiki.org/wiki/Extension:PubmedParser | http://www.mediawiki.org/wiki/Extension:PubmedParser | ||
| + | === BiblioPlus === | ||
| + | |||
| + | * https://www.mediawiki.org/wiki/Extension:BiblioPlus | ||
| + | * 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 == | ||
Latest revision as of 16:33, 21 January 2022
To-do list
- Contribution credits?
- Write a history/timeline page
- NewUserMessage could be good
- Static pages?
- RSS feeds for all pages?
- Should use MultiBoilerplate at some point!
- Add LookupUser extension, maybe UserSnoop
- Add ContactPage extension (consider captch implementation)
- Performance tuning
- User Contact Links looks slick.
- Who Is Watching pages?
- http://www.mediawiki.org/wiki/Extension:WhoIsWatchingTabbed
- see also also related extensions on that 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
Sitesubtitle - Edited, not sure of the effect...
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
- https://www.mediawiki.org/wiki/Extension:BiblioPlus
- 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
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
- All seems OK
- reCaptcha works on all pages, including Special:Contact (must not be logged in as sysop to see it) and 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).
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).
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)
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
- 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 189 GH family pages and 33 lexicon pages.
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
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)
Harry Brumer 13:48, 8 November 2009 (UTC)
Implemented Template:Smallcaps
- Wraps some markup for simple implementation of small caps, e.g. for use in d/l sugar nomenclature.
- NOTE (from the [http://en.wikipedia.org/wiki/Template:Smallcaps/doc Smallcaps template doc page):
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>
- However, not really pretty. Extension disabled.
- Might use DynamicPageList2: http://www.mediawiki.org/wiki/Extension:DynamicPageList_(third-party)
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.
{{#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.
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
- ...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
- 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.
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)