Proxying Galaxy with Apache httpd Rewrite?

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I was setting up Apache using the instructions in the link. Proxying Galaxy with Apache — Galaxy Project 23.1.1.dev0 documentation
However, my sysadmin said that it does not work the way the site said.

When you use the RewriteRule:

RewriteRule Pattern Substitution

both Pattern and Substitution are supposed to be URL paths. But you
were using a filesystem path (/peopleroot/…). That’s why it couldn’t
be found.

What you want there is an Alias. I added the following to your config:

Alias “/static” “/peopleroot/skim/galaxy/static”
Alias “/static/style” “/peopleroot/skim/galaxy/static/style/blue”
Alias “/favicon.ico” “/peopleroot/skim/galaxy/static/favicon.ico”
Alias “/robots.txt” “/peopleroot/skim/galaxy/static/robots.txt”
Alias “/plugins” “/peopleroot/skim/galaxy/config/plugins”

See:

https://server.mb.re.kr/favicon.ico
https://server.mb.re.kr/plugins/visualizations/scatterplot/static/logo.png

However, some URLs:

https://server.mb.re.kr/plugins/visualizations/scatterplot/static/scatterplot.css

return a 404 with the message, “This link may not be followed from
within Galaxy.”

Galaxy source code says the error is “Called on any url that does not
match a controller method”.

I’m not sure what that’s about, but I found this discussion:

Fresh Install Has Wrong Layout

Is it possible to know what is the correct way to do this?
Now the favicon.ico works, but the main website does not load…

Current httpd conf for :443
#
# This configuration file is for HTTPS (port 443).
#
#
# IMPORTANT: Run this as root after making any changes:
#
# /usr/local/psa/admin/bin/httpdmng --reconfigure-domain server.mb.re.kr
#

# use a variable for convenience
# NB: mod_define is only for Apache 2.4+.
#Define galaxy_root /peopleroot/skim/galaxy

#
# set up for proxies
#
ProxyRequests Off
SetOutputFilter proxy-html
SSLProxyEngine On
# don't decode encoded slashes in path info
AllowEncodedSlashes On

# enable compression on all relevant types
AddOutputFilterByType DEFLATE text/html text/plain text/xml
AddOutputFilterByType DEFLATE text/css
AddOutputFilterByType DEFLATE application/x-javascript application/javascript application/ecmascript
AddOutputFilterByType DEFLATE application/rss+xml
AddOutputFilterByType DEFLATE application/xml
AddOutputFilterByType DEFLATE application/json

# allow access to static content
Alias "/static" "/peopleroot/skim/galaxy/static"
<Directory "/peopleroot/skim/galaxy/static">
    AllowOverride None
    Require all granted
</Directory>
Alias "/static/style" "/peopleroot/skim/galaxy/static/style/blue"
Alias "/favicon.ico" "/peopleroot/skim/galaxy/static/favicon.ico"
Alias "/robots.txt" "/peopleroot/skim/galaxy/static/robots.txt"

# Galaxy needs to know that this is https for generating URLs
RequestHeader set X-URL-SCHEME "%{REQUEST_SCHEME}e"

# allow up to 6 minutes for Galaxy to respond to slow requests before timing out
ProxyTimeout 360

# or uWSGI on a TCP socket
ProxyPass / uwsgi://127.0.0.1:4432/ nocanon

# serve framework static content
#RewriteEngine On
# THE FOLLOWING IS WRONG:
#RewriteRule ^/static/style/(.*) /peopleroot/skim/galaxy/static/style/blue/$1 [L]
#RewriteRule ^/static/(.*) /peopleroot/skim/galaxy/static/$1 [L]
#RewriteRule ^/favicon.ico /peopleroot/skim/galaxy/static/favicon.ico [L]
#RewriteRule ^/robots.txt /peopleroot/skim/galaxy/static/robots.txt [L]

# enable caching on static content
<Location "/static">
    ExpiresActive On
    ExpiresDefault "access plus 24 hours"
</Location>

Alias "/plugins" "/peopleroot/skim/galaxy/config/plugins"
<Directory "/peopleroot/skim/galaxy/config/plugins">
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>

# serve visualization and interactive environment plugin static content
<Directory "/peopleroot/skim/galaxy/config/plugins/(.+)/(.+)/static">
    AllowOverride None
    Require all granted
</Directory>
# THE FOLLOWING IS WRONG:
#RewriteRule ^/plugins/(.+)/(.+)/static/(.*)$ /peopleroot/skim/galaxy/config/plugins/$1/$2/static/$3 [L]
1 Like
2

No Apache expert here, but the documentation of Apache clearly states

The mod_rewrite module uses a rule-based rewriting engine, based on a PCRE regular-expression parser, to rewrite requested URLs on the fly. By default, mod_rewrite maps a URL to a filesystem path. However, it can also be used to redirect one URL to another URL, or to invoke an internal proxy fetch.

So I think the galaxy documentation is correct.

1 Like