Help:Contents: Difference between revisions

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==Upgrading MediaWiki==
<big>Step 1</big> '''- [http://www.mediawiki.org/wiki/Manual:Upgrading download latest stable version of MediaWiki]'''
<big>Step 2</big> '''- determine database credentials from dreamhost'''
;Get Hostname (e.g.):
* mysql.bradleymonk.com
;Get Database name (e.g.):
* bradleymonk_com
;Get Database User name (e.g.):
* username
;Get Database User pass (e.g.):
* password
<big>Step 3</big> '''- back-up existing files and the database'''
*Go to: mysql.example.com
*Enter db user and password when prompted
*click on db in left panel
*click on the "Export" tab
*check "Save as file"
*click "Go"
<big>Step 4</big> '''- FTP the <code>mediawiki.tar.gz</code> file to the /w directory'''
<big>Step 5</big> '''- Unpack the tarball'''
;Use the console to SSH into the /w directory and unpack tarball
* <code>$ssh bradleymonk.com -l username</code>
* Change to the /w directory
:* <code>$tar xvzf mediawiki.tar.gz</code>
*this unpacks into a new folder: <code>/w/mediawiki</code>
<big>Step 6</big> '''- Move files and rename directory'''
;Copy files from old to new directory
* LocalSettings.php
* logofile.png
* images (or upload) directory
* extension directory
* custom skins
* .htaccess file
;Swap-rename directories
*rename old directory <code>/w_old</code>
*move new directory out of <code>/w_old</code> to top level domain
*rename new directory to <code>/w</code>
<big>Step 7</big> '''- Run MediaWiki update script'''
* login with SSH again:
:* <code>$ssh bradleymonk.com -l username</code>
* change to the <code>/w/maintenance</code> directory
* enter: <code>$php update.php</code>
* If the prompt gives an error like: "you're using php version 2.x mediawiki requires version 3.x"
* try entering these:
:* <code>$/usr/local/php53/bin/php update.php</code>
:* <code>$/usr/local/php54/bin/php update.php</code>
;Check if the upgrade worked by going to the MediaWiki page "Special Version"




[[Category:Templates]]
[[Category:Templates]]

Revision as of 17:52, 8 July 2013

MediaWiki Help Pages

Bradleymonk.com .JS

Template:SlideBox

{{SlideBox|width=80%|float=left|
Header Content Is Shown
|
Body text is hidden
}}

Customize Editing Toolbar

http://bradleymonk.com/User:Bradley_Monk/common.js http://www.mediawiki.org/wiki/Extension:WikiEditor/Toolbar_customization

section
  • {String} (optional) The name of the section in the WikiEditor. Defaults to 'main'
id
  • {String} (required) Unique id (ie. 'my-button')
icon
  • {String} (recommended) URL to the icon, should be square about 21 to 22px
label
  • {String} (required) Tooltip displayed when hovering button
insertBefore
  • {String} (optional) Wikitext to be inserted before the cursor on-click
sampleText
  • {String} (optional) Text inserted in place of the cursor if no text was selected
insertAfter
  • {String} (optional) Wikitext to be inserted after the cursor on-click
callback
  • {Function} (optional) Called when the button is clicked
autoSummary
  • {mixed} (optional) Null or an Object with the following properties:
    • summary: {String} (required) Edit summary that should be used
    • position: {String} (optional) 'append', 'prepend' or 'replace'
    • delimiter: {String} (optional) delimiter between the (possibly) current summary and the to-be-inserted summary

Image Annoation

<div class="wpImageAnnotatorEnable">
<span class="wpImageAnnotatorPageName" style="display:none;">Sandbox</span>
<span class="wpImageAnnotatorFullName" style="display:none;">Sandbox</span>
<div class="wpImageAnnotatorFile">[[File:Foo.png]]</div>
<div style="display:none;"><div><div><!--IMAGE NOTES BELOW -->{{ImageNoteEnd|id=-1}}
</div>

Livelets

To create livelets, wrap any areas of the page in the #live parser-function.

In the following example, a transclusion of the page called Template:MyVerySlowTable has been turned into a livelet: 

{{#live: {{MyVerySlowTable}} }}


References and Citations

In-text references make it easy to copy the text to another page; on the other hand, they make it hard to read. References containing a lot of data, quotes or elaborate citation templates can make up a significantly larger fraction of the source than the text that will actually be visible. To avoid this, recent versions of the extension allow moving some or all of the references into the <references /> section, to the place where they will actually appear to the reader. Thus,

According to scientists, the Sun is pretty big.<ref name="miller" />
The Moon, however, is not so big.<ref name="smith" />

==Notes==
<references>
<ref name="miller">E. Miller, The Sun, (New York: Academic Press, 2005), 23-5.</ref>
<ref name="smith">R. Smith, "Size of the Moon", Scientific American, 46 (April 1978): 44-6.</ref>
</references>

will have the same output as the first example above, although the numbering and order of the references will not in general be the same.


HTML

Example

<html> <iframe src="http://www.w3schools.com/tags/tag_iframe.asp" height="100" width="400" frameborder="1" seamless="seamless" style="float:left"></iframe> </html>

iFrame Code 

<html>
<iframe src="http://www.w3schools.com/tags/tag_iframe.asp" 
height="300" width="350" frameborder="1" seamless="seamless" style="float:left">
</iframe>
</html>

iFrame Attributes

Attribute Value Description
align left, right, top, middle, bottom Specifies the alignment of an iframe according to surrounding elements
frameborder 1, 0 Specifies whether or not to display a border around an iframe
height pixels Specifies the height of an iframe
longdesc URL Specifies a page that contains a long description of the content of an iframe
marginheight pixels Specifies the top and bottom margins of the content of an iframe
marginwidth pixels Specifies the left and right margins of the content of an iframe
name name Specifies the name of an iframe
sandbox "", allow-forms, allow-same-origin, allow-scripts, allow-top-navigation Enables a set of extra restrictions for the content in the iframe
scrolling yes, no, auto Specifies whether or not to display scrollbars in an iframe
seamless seamless Specifies that the iframe should look like it is a part of the containing document
src URL Specifies the address of the document to embed in the iframe
srcdoc HTML_code Specifies the HTML content of the page to show in the iframe
width pixels Specifies the width of an iframe

Tables

wikitable

Link Description
BioNetGen A web-based tool for automatically generating a biochemical reaction networks from user-specified rules for biomolecular interactions.
B10NUMB3R5 (BIONUMBERS) A database of useful biological numbers.
BioInformatics Services BioInformatics Services is a biotechnology consulting firm specializing in using computational biology to solve complex biological and data analysis problems.
cellmigrationgateway modeling software
CellML The CellML language is an open standard based on the XML markup language at the University of Auckland and affiliated research groups.
CompCell Bio Web Development site for teaching modules on quantitative cell biology.
DOQCS Quantitative Cellular Signaling (DOQCS) is a repository of models of signaling pathways.
E-Cell A Multi-Algorithm, Multi-Timescale Simulation Software Environment.
Gfit A program for global regression analysis of experimental data.
Kitware Professional Visualization Solutions, Tools and Support.
MCell General Monte Carlo Simulator of Cellular Microphysiology.
Minimotif Miner Application to search for short sequence motifs in Proteins.


Upgrading MediaWiki

Step 1 - download latest stable version of MediaWiki


Step 2 - determine database credentials from dreamhost

Get Hostname (e.g.)
  • mysql.bradleymonk.com
Get Database name (e.g.)
  • bradleymonk_com
Get Database User name (e.g.)
  • username
Get Database User pass (e.g.)
  • password


Step 3 - back-up existing files and the database

  • Go to: mysql.example.com
  • Enter db user and password when prompted
  • click on db in left panel
  • click on the "Export" tab
  • check "Save as file"
  • click "Go"


Step 4 - FTP the mediawiki.tar.gz file to the /w directory


Step 5 - Unpack the tarball

Use the console to SSH into the /w directory and unpack tarball
  • $ssh bradleymonk.com -l username
  • Change to the /w directory
  • $tar xvzf mediawiki.tar.gz
  • this unpacks into a new folder: /w/mediawiki


Step 6 - Move files and rename directory

Copy files from old to new directory
  • LocalSettings.php
  • logofile.png
  • images (or upload) directory
  • extension directory
  • custom skins
  • .htaccess file
Swap-rename directories
  • rename old directory /w_old
  • move new directory out of /w_old to top level domain
  • rename new directory to /w


Step 7 - Run MediaWiki update script

  • login with SSH again:
  • $ssh bradleymonk.com -l username
  • change to the /w/maintenance directory
  • enter: $php update.php


  • If the prompt gives an error like: "you're using php version 2.x mediawiki requires version 3.x"
  • try entering these:
  • $/usr/local/php53/bin/php update.php
  • $/usr/local/php54/bin/php update.php


Check if the upgrade worked by going to the MediaWiki page "Special Version"
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