.htaccess

##
# @package    Joomla
# @copyright  Copyright (C) 2005 - 2017 Open Source Matters. All rights reserved.
# @license    GNU General Public License version 2 or later; see LICENSE.txt
##

##
# READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE!
#
# The line 'Options +FollowSymLinks' may cause problems with some server configurations.
# It is required for the use of mod_rewrite, but it may have already been set by your 
# server administrator in a way that disallows changing it in this .htaccess file.
# If using it causes your site to produce an error, comment it out (add # to the 
# beginning of the line), reload your site in your browser and test your sef urls. If 
# they work, then it has been set by your server administrator and you do not need to 
# set it here.
##

## No directory listings
<IfModule autoindex>
  IndexIgnore *
</IfModule>

## Can be commented out if causes errors, see notes above.
Options +FollowSymlinks
Options -Indexes

## Mod_rewrite in use.

RewriteEngine On

# WP REST API BLOCK JSON REQUESTS
# Block/Forbid Requests to: /wp-json/
RewriteCond %{REQUEST_URI} ^.*wp-json/ [NC]
RewriteRule ^(.*)$ - [F]

#After trying to enable HTTPS by default in the entire site using JOOMLA! interface
#it failed, so the following two lines do that
RewriteCond %{HTTPS} off
RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [R=301,NC,L]

#Remove the www. from the URL - Only in PROD
#RewriteCond %{HTTP_HOST} ^www.reactome.org
#RewriteRule (.*) https://reactome.org/$1 [R=301,L]

## Begin - Rewrite rules to block out some common exploits.
# If you experience problems on your site then comment out the operations listed 
# below by adding a # to the beginning of the line.
# This attempts to block the most common type of exploit `attempts` on Joomla!
#
# Block any script trying to base64_encode data within the URL.
RewriteCond %{QUERY_STRING} base64_encode[^(]*\([^)]*\) [OR]
# Block any script that includes a <script> tag in URL.
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
# Block any script trying to set a PHP GLOBALS variable via URL.
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block any script trying to modify a _REQUEST variable via URL.
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Return 403 Forbidden header and show the content of the root home page
RewriteRule .* index.php [F]
#
## End - Rewrite rules to block out some common exploits.

## Begin - Custom redirects
#
# If you need to redirect some pages, or set a canonical non-www to
# www redirect (or vice versa), place that code here. Ensure those
# redirects use the correct RewriteRule syntax and the [R=301,L] flags.

Redirect 301 /pages/about/reactome /what-is-reactome
Redirect 301 /pages/about/news /about/news
Redirect 301 /pages/about/reactome-team /about/team
Redirect 301 /pages/about/reactome-scientific-advisory-board /sab
Redirect 301 /pages/about/license-agreement /license
Redirect 301 /pages/about/reactome-disclaimer /about/disclaimer
Redirect 301 /pages/about /what-is-reactome

Redirect 301 /stats.html /about/statistics

Redirect 301 /pages/content/orcid-integration-project /orcid

Redirect 301 /pages/documentation/developer-guide/graph-database/tutorial-participating-molecules /dev/graph-database/extract-participating-molecules
Redirect 301 /pages/documentation/developer-guide/diagram/diagram-js /dev/diagram/js
Redirect 301 /pages/documentation/developer-guide/diagram/diagram-gwt /dev/diagram/gwt
Redirect 301 /pages/documentation/developer-guide/pathways-overview/fireworks-js /dev/pathways-overview/js
Redirect 301 /pages/documentation/developer-guide/pathways-overview/fireworks-gwt /dev/pathways-overview/gwt
Redirect 301 /pages/documentation/developer-guide/analysis-service /dev/analysis
Redirect 301 /pages/documentation/developer-guide/content-service /dev/content-service
Redirect 301 /pages/documentation/developer-guide/graph-database /dev/graph-database
Redirect 301 /pages/documentation/developer-guide/diagram /dev/diagram
Redirect 301 /pages/documentation/developer-guide/pathways-overview /dev/pathways-overview
Redirect 301 /pages/documentation/developer-guide/partners /community/partners

Redirect 301 /pages/documentation/data-model /documentation/data-model
Redirect 301 /pages/documentation/electronically-inferred-events /documentation/inferred-events
Redirect 301 /electronic_inference.html /documentation/inferred-events
Redirect 301 /electronic_inference_compara.html /documentation/inferred-events
Redirect 301 /pages/documentation/linking-to-reactome /linking-to-us
Redirect 301 /pages/documentation/linking-to-reactome/list-of-identifiers /linking-to-us/identifiers
Redirect 301 /pages/documentation/citing-reactome-publications /cite
Redirect 301 /pages/documentation/developer-guide /dev
Redirect 301 /pages/documentation /documentation

Redirect 301 /pages/community/outreach /community/outreach
Redirect 301 /pages/community/reactome-events /community/events
Redirect 301 /pages/community/reactome-publications /community/publications
Redirect 301 /pages/community/training /community/training
Redirect 301 /pages/download-data /download-data

Redirect 301 /download/tools/curatorTool/install.htm /download-data/reactome-curator-tool
Redirect 301 /user/reactome-fiviz /tools/reactome-fiviz

Redirect 302 /user/guide /userguide

# Used in PAPERS
Redirect 301 /tutorials/pwp https://youtu.be/-skixrvI4nU
Redirect 301 /documentation/index.php/Glossary_Data_Model /documentation/data-model
#Redirect 301 /cgi-bin/classbrowser /content/schema

# Redirect eventbrowser to content/detail
RewriteCond %{REQUEST_URI}  ^/cgi-bin/eventbrowser*$
RewriteCond %{QUERY_STRING} ^ST_ID=((R-[A-Z]{3}-[0-9].*)|(REACT_\d+.*))$
RewriteRule ^(.*)$ /content/detail/%1? [R=301,L]

RewriteCond %{REQUEST_URI}  ^/cgi-bin/eventbrowser_st_id*$
RewriteCond %{QUERY_STRING} ^ST_ID=((R-[A-Z]{3}-[0-9].*)|(REACT_\d+.*))$
RewriteRule ^(.*)$ /content/detail/%1? [R=301,L]

# Redirect author_contributions to /content/detail/person
RewriteCond %{REQUEST_URI}  ^/cgi-bin/author_contributions*$
RewriteCond %{QUERY_STRING} ^DB=(.*)&ID=([0-9]*)\&?$
RewriteRule ^(.*)$ /content/detail/person/%2? [R=301,L]

RewriteCond %{REQUEST_URI}  ^/cgi-bin/author_contributions*$
RewriteCond %{QUERY_STRING} ^ID=([0-9]*)$
RewriteRule ^(.*)$ /content/detail/person/%1? [R=301,L]

# Redirect doi/toc old cgis to /content/doi /content/toc
RewriteCond %{REQUEST_URI}  ^/cgi-bin/doi_toc*$
RewriteCond %{QUERY_STRING} ^DB=(.*)$
RewriteRule ^(.*)$ /content/doi? [R=301,L]

RewriteCond %{REQUEST_URI}  ^/cgi-bin/toc*$
RewriteCond %{QUERY_STRING} ^DB=(.*)$
RewriteRule ^(.*)$ /content/toc? [R=301,L]

# Forbidding any url access for the user login component
RewriteRule index.php/staff index.php [F]
RewriteRule index.php/component/users index.php [F]
#RewriteRule component/users index.php [F]

#RewriteCond %{QUERY_STRING} (^|&)option=com_users(&|$)
#RewriteRule ^(.*) - [F]

# Servers only
#Redirect 301 /staff  /
#Redirect 301 /administrator  /

## End - Custom redirects

##
# Uncomment the following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root).
##
# RewriteBase /

## Begin - Joomla! core SEF Section.
#
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
#
# If the requested path and file is not /index.php and the request
# has not already been internally rewritten to the index.php script
RewriteCond %{REQUEST_URI} !^/index\.php
# and the requested path and file doesn't directly match a physical file
RewriteCond %{REQUEST_FILENAME} !-f
# and the requested path and file doesn't directly match a physical folder
RewriteCond %{REQUEST_FILENAME} !-d
# internally rewrite the request to the index.php script
RewriteRule .* index.php [L]
#
## End - Joomla! core SEF Section.

# Enable PHP Logs - uncomment the following to DEBUG php.
# Comment once the issue is addressed.
#php_flag display_errors on