biostor-classic
BioStor provides tools for extracting, annotating, and visualising literature from the Biodiversity Heritage Library (and other sources). For background and further details please see:
Page, R. D. (2011). Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library. BMC Bioinformatics. Springer Science + Business Media. http://dx.doi.org/10.1186/1471-2105-12-187
This repository is the original site (PHP + MySQL + Solr), with minor modifications as site is moved to new server.
Notes on installing BioStor (classic) from scratch
VirtualHostX
httpd-vhosts.conf
NameVirtualHost *:80
<Directory “/Users/rpage/Sites/biostor-classic/www/“> Allow From All AllowOverride All Options +Indexes Require all granted <VirtualHost 130.209.46.59:80> ServerName “biostor.org” DocumentRoot “/Users/rpage/Sites/biostor/www”
MySQL
http://stackoverflow.com/a/7264459
If you have /tmp/mysql.sock but no /var/mysql/mysql.sock then…
cd /var
sudo mkdir mysql
sudo chmod 755 mysql
cd mysql
ln -s /tmp/mysql.sock mysql.sock
If you have /var/mysql/mysql.sock but no /tmp/mysql.sock then
cd /tmp
ln -s /var/mysql/mysql.sock mysql.sock
You will need permissions to create the directory and link, so just prefix the commands above with sudo if necessary.
cache
If image files are being stored on same hard drive as web server, then make sure www/cache is writable by web server.
If cache is on another drive, make www/cache a symbolic link to external drive (drive also needs to be writable by web server.
ImageMagick
You need ImageMagick installed, and the path to the convert executable specified in config.inc.php. You need support for GIF, JPG, PNG, and TIFF.
You can get a Mac OS X installer from CactusLabs http://cactuslab.com/imagemagick/, but this generates “convert: Saving binary kernel failed” errors.
Installed using HomeBrew http://brew.sh There have been issues reported with ImageMagick and HomeBrew, e.g. http://stackoverflow.com/questions/5624778/imagemagick-jpeg-decode-delegate-missing-with-os-x-homebrew-install. This worked for me:
brew install —force jpeg
brew install —force imagemagick
ExifTools
To add metadata to PDFs we need ExifTools by Phil Harvey. Download and install the Mac OS X Package.
Apache configuration
Make sure to uncomment
LoadModule rewrite_module libexec/apache2/mod_rewrite.so
in httpd.conf.
In .htaccess in the www folder, add:
# Rewrite /foo/bar to /foo/bar.php
RewriteRule ^openurl\??$ %{REQUEST_URI}.php [L]
(from http://php.net/manual/en/security.hiding.php). This ensures the URL /openurl will work.
mysqlbigram
We create a bigram index on the bhl_title table to help search for journal matches. This requires a MySQL plugin to support bigram searches.
Grab mysqlbigram from https://sites.google.com/site/mysqlbigram/
The code expects to find the mysql header files in /usr/local/include, so I created a symbolic link:
cd /usr/local/include
sudo ln -s /usr/local/mysql/include mysql
Then
./configure --prefix=/usr/local
make
sudo make install
The plugin is installed by default in
/usr/local/lib/mysql/
MySQL expects these in
/usr/local/mysql/lib/plugin/
so we move them
cd /usr/local/lib/mysql/
sudo cp * /usr/local/mysql/lib/plugin/
Edit my.cnf - on my Mac running Yosemite this is located here:
/usr/local/mysql-5.6.21-osx10.8-x86_64/my.cnf
Add these lines:
[mysqld]
ft_min_word_len=1
Restart MySQL, then run this query to install plugin:
INSTALL PLUGIN bi_gram SONAME ‘bi_gramlib.so’;
verify with command:
SHOW PLUGINS;
This enables us to create the bhl_title table:
CREATE TABLE `hl_title` (
`TitleID` int(11) NOT NULL DEFAULT ‘0’,
`MARCBibID` varchar(50) DEFAULT NULL,
`MARCLeader` varchar(24) DEFAULT NULL,
`FullTitle` text,
`ShortTitle` varchar(255) DEFAULT NULL,
`PublicationDetails` varchar(255) DEFAULT NULL,
`CallNumber` varchar(100) DEFAULT NULL,
`StartYear` int(11) DEFAULT NULL,
`EndYear` int(11) DEFAULT NULL,
`LanguageCode` varchar(10) DEFAULT NULL,
`TL2Author` varchar(100) DEFAULT NULL,
`TitleURL` varchar(100) DEFAULT NULL,
PRIMARY KEY (`TitleID`),
FULLTEXT KEY `ShortTitle_2` (`ShortTitle`) /*!50100 WITH PARSER `bi_gram` */
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
MySQL configuration file
Most tools seem to expect the file my.cnf to be in /etc, so we can create a symbolic link:
sudo ln -s /usr/local/mysql/my.cnf
Image cache
In the www directory there should be a folder called “cache”. This can be a physical folder while setting up, but in production the images will be stored on an external hard drive. Create a symbolic link to the external drive, and make sure it the link permissions are correct. For example:
cd www
ln -s /Volumes/LaCie/WebServer/biostor/cache cache
chmod 777 cache
ini_set(‘mysql.connect_timeout’, 300); ini_set(‘default_socket_timeout’, 300);