Help:Setting up this wiki

From BiodivBorneo09

Setting up a new Axioo pico as a Wiki server

Install Fedora 10 (I used Omega remix)
Get the system updated

# yum groupupdate Base
* yum install kernel

Switch off SELinux
Get needed software

# yum install ImageMagick php mysql mysql-server php-mysql

Reboot
Activate httpd and mysqld from the Services admin tool
Reboot (seems to be needed to get MySql to start
Edit httpd.conf, changing the following in the appropriate places:

...
DocumentRoot "/var/www/html/wiki/"
...
<Directory "/var/www/html/wiki">
...
Options Indexes FollowSymLinks ExecCGI
...

Set up MySql database

# mysqladmin create bb09
# mysql bb09
...
mysql> create user 'bb09'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> grant all on bb09.* to 'bb09'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> set password for 'bb09'@'localhost' = password('########');
Query OK, 0 rows affected (0.00 sec)

mysql> \q

Unzip the new mediawiki distrib

# cd /var/www/html
# tar xvzf mediawiki-1.14.0.tar.gz
# mv mediawiki-1.14.0 wiki

Set permissions (maybe needed by by suexec)

# chown -R apache wiki
# chgrp -R apache wiki
# chmod -R go-w wiki

Point your browser at http://localhost, and proceed with the install as directed
Copy LocalSettings.php from config/ up one directory
Edit a few things in LocalSettings.php

$wgEnableUploads       = true;
$wgLogo = "/images/c/c1/BOB2009logo.png" ;
$wgGroupPermissions['*']['edit'] = false;
$wgFileExtensions = array( 'png', 'gif', 'jpg', 'jpeg', 'pdf', 'txt' );

Finally, set the max file upload size in /etc/php.ini:

; Maximum allowed size for uploaded files.                                      
upload_max_filesize = 500K

Backing up the wiki

It seems the three parts of backing up are:

Backing up the physical PHP and image directories:

# tar cvzf 2009-06-01_wiki.tgz wiki
... or ...
# rsync -avP --delete wiki/ cwebb@phylodiversity.net:backup/bb09wiki/

Backing up the mySQL database:

# mysqldump bb09 > ~/backup/2009-06-01_bb09.sql

Backing up the Wiki via its XML form

# php maintenance/dumpBackup.php --current > ~/backup/2009-06-01_bb09.xml

In fact, here's a script (backup.sh) to help. Place in /var/www/html:

#!/bin/sh                                                                       
DATE=`date "+%F"`
php wiki/maintenance/dumpBackup.php --full > wiki/backup/$DATE.xml
mysqldump bb09 > wiki/backup/$DATE.sql
rsync -avzP --delete wiki/ bb09@phylodiversity.net:WEBSITE/wiki/

A live wiki should be made readonly while backing up with:

$wgReadOnly = 'Temporarily locked: backing up';

Restoring (mirroring) to Dreamhost

Make sure the newest version is rsync'd into place
Create a new empty mysql DB with the control panel. If existing, drop all tables (thanks for this post):

# mysql -h mysql.phylodiversity.net -ucwebb -pfoo testdb -e "show tables" | \
  grep -v Tables_in | grep -v "+" | \
  gawk '{print "drop table " $1 ";"}' | \
  mysql -h mysql.phylodiversity.net -ucwebb -pfoo testdb

Log into bb09@phylodiversity.net and cd to the wiki directory
Load the data:

mysql -h mysql.phylodiversity.net -u foo -pfoo wikidb < backup/2009-06-01.sql

For dreamhost, make sure php5 is being used by adding a .htaccess file:

Options +ExecCGI
AddHandler php5-cgi .php

Edit the LocalSettings.php (from diff output):

> $wgScriptPath       = "/bb09/wiki";
...
> $wgDBserver         = "mysql.phylodiversity.net";
> $wgDBname           = "testdb";
> $wgDBuser           = "foo";
> $wgDBpassword       = "foo";
...
> $wgLogo = "/bb09/wiki/images/c/c1/BOB2009logo.png" ;

Make sure the images directory is writable:

$ find images -type d -execdir chmod g+w '{}' \;

Note: PdfExport does not work because of lack of htmldoc (also set temp dir on L40 of extensions/PdfExport/PdfExport_body.php. Also may need to fiddle to get Math working, due to lack of installed ocaml, etc. Set

$wgUseTeX = false ;

Best to leave the public mirror readonly:

$wgReadOnly = 'This is a mirror';

PDF Export

A nice extension; another, untried tool is wikipdf.

Install htmldoc with yum
Create a directory called PdfExport in extensions
Copy files from here to the four files indicated
Make a new tmp directory:

# mkdir /var/www/tmp
# chown apache /var/www/tmp

Edit lines in PdfExport_body.php. Edit:

$mytemp = "/var/www/tmp" . "/f" .time(). "-" .rand() . ".html";

and replace:

$bhtml = str_replace ($wgScriptPath, $wgServer . $wgScriptPath, $bhtml);

with:

$bhtml = str_replace ("href=\"/index.php", "href=\"" . $wgServer . "/index.php", $bhtml); 
$bhtml = str_replace ("src=\"/images", "src=\"" . $wgServer . "/images", $bhtml);

(Thanks to comments on the discussion page for Pdf_Export)

Add to LocalSettings.php

require_once("extensions/PdfExport/PdfExport.php");

Semantic MediaWiki

(See excellent directions here)

Untar the latest release of this important extension into extensions
Add these lines to LocalSettings.php:

include_once("$IP/extensions/SemanticMediaWiki/includes/SMW_Settings.php");
enableSemantics('phylodiversity.net');

Log in as admin and go to Special:SMWAdmin
Click `build tables,' then `repair data' (wait a long time), and all should be functioning.

Maths

(See here for details)

Install some extras, and build:

# yum install yum install ocaml gv dvipng dvips texlive texlive-latex
# cd math
# make

Edit LocalSettings.php

$wgUseTeX = true ;

Include LaTeX maths expressions. <math>\int\limits_a^x f(\frac{\alpha}{2}\,)\,dx</math> is created by:

<math>\int\limits_a^x f(\frac{\alpha}{2}\,)\,dx</math>

See this guide to LaTeX maths markup.

File sharing

SAMBA

# yum install samba system-config-samba samba-swat

Start smb and swat with Services. A reboot may be needed. Be sure to allow samba through the firewall (Admin -> Firewall).
Create special users for files. It seems to easy to expose the entire home directory for a subdirectory.

# system-config-samba &

Set up a samba user for existing users. A working /etc/samba/smbusers is:

root = administrator admin
nobody = guest pcguest smbguest
files = files
share = share

Add samba shares. A working /etc/samba/smb.conf is:

[global]
	workgroup = bb09files
	server string = Samba Server Version %v
	log file = /var/log/samba/log.%m
	max log size = 50
	security = user
	passdb backend = tdbsam
	cups options = raw
	username map = /etc/samba/smbusers
	guest ok = yes
[homes]
	comment = Home Directories
	browseable = no
	writable = yes
[printers]
	comment = All Printers
	path = /var/spool/samba
	browseable = no
	printable = yes
[BB09FILESW]
	comment = BB09 resources writable
	path = /home/files
	writeable = yes
	valid users = files
[BB09FILES]
	comment = BB09 resources
	path = /home/files
	valid users = share
[BB09SHARE]
	comment = Filesharing area
	path = /home/share
	writeable = yes
	valid users = share

Alternatively, use swat by browsing to http://localhost:901/.
Now, access possible with smb://192.168.1.100/ or smb://192.168.1.5/bb09files/ for a specific shares.

HTTP access

In httpd.conf add an alias:

Alias /bb09files/ "/home/files/"

<Directory "/home/files">
    Options Indexes MultiViews FollowSymLinks
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>

Files (or directories) can now be accessed with direct URL links. Use links of the form [http://{{SERVERNAME}}/bb09files/] so that they work when the wiki is migrated to a different server. I.e., our files top directory.

Other extensions installed

CategoryTree
Cite^[1]
DumpHTML. Dump with:

cd /var/www/html/wiki/extensions/DumpHTML
php dumpHTML.php -d /var/www/html/static -k monobook --image-snapshot --show-titles
find /var/www/html/static -name "Talk~*" -exec rm -v '{}' \; # deletes talk pages
cp -a ../../skins /var/www/html/static/.
tar chvzf bb09.tgz /var/www/html/static # -h for deref symlinks
# rsync -aPL /var/www/html/static/ bb09@phylodiverity.net:static/

CSS tweaks

I didn't like some of the original choices in monobook. Here are my new values (changes only):

 h1, h2, h3, h4, h5, h6 {
        /*border-bottom: 1px solid #aaa; */  /* drop */
}
h2 { font-size: 160%;     /* bigger */
     font-weight: bold;   /* bold */
     margin-top: 1em;     /* more */
}
h3 { font-size: 120%; }   /* smaller */

To do differently next time

Make the student home pages be their User:Foo page.

Footnotes

↑ The footnote

[0] The footnote

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