Mook - CSBE Web Server

General

Mook is SynthSys ' web and application server. It has 3 aliases in the DNS - mook.inf.ed.ac.uk, csbe.inf.ed.ac.uk, synthsys.inf.ed.ac.uk. There is a signed Comodo SSL certificate for it as synthsys.inf.ed.ac.uk. All 3 of those redirect to https://synthsys.inf.ed.ac.uk/

It currently hosts the following subsites:

https://synthsys.inf.ed.ac.uk/twiki - Centre Wiki
https://synthsys.inf.ed.ac.uk/bugs - Bugzilla tracker
https://synthsys.inf.ed.ac.uk/bookings - Centre room booking system
https://synthsys.inf.ed.ac.uk/biosched - Second booking system for lab equipment
https://synthsys.inf.ed.ac.uk/gengy - phpMyAdmin for Gengy

These were looked after by Informatics but local staff have admin rights to manage users

Additionally the following VHosts are served from Mook via AJP Tomcat apps:

http://www.biodare.ed.ac.uk
http://www.plasmo.ed.ac.uk
http://www.sbsi.ed.ac.uk

The following is a "plain" VHost that is externally managed by a commercial company, but hosted on mook:

http://www.timing-metabolism.eu

Mook does not host the man centre website - www.synthsys.ed.ac.uk

Finally, it is also used as a compute server for users to SSH into and run Matlab jobs on remotely. These use the standard DICE Matlab headers and licenses, of which CSBE have paid for ~10 some of which are reserved on our matlab-research license server

Webapps

Mook runs a number of self-managed Tomcat instances, plus one partly-managed instance, some of which are responsible for serving the websites mentioned above. Users have the ability to su tomcat & su apache and manage their software themselves.

These are many and varied - see the machine's LCFG profile for most up to date list.

Reinstall

Mostly LCFG'd. One exception is requiring a symlink for a user-library that has a static path:

ln -s /disk/data/robust/fft_tz/libFFTParallel.so /usr/lib/libFFTParallel.so

ln -s /disk/data/robust/fft_tz/libFFT.so /usr/lib/libFFT.so

See RT#58923 - check with tzielins if this is still required

Bugzilla:

nsu

cd /disk/data/web/html/bugs/

/usr/bin/perl install-module.pl --all

./checksetup.pl

Autostarts

apache - via LCFG component

Matlab - n/a

tomcat x5 - via Cron jobs

Details

Apache

Autostarts on boot

Locations

Configuration:

/disk/data/web/conf/

DocumentRoot :

/disk/data/web/html

SSL Conf

/etc/httpd/conf.d/ssl.conf

SSL Certs

SSLCertificateFile /etc/pki/tls/certs/synthsys.inf.ed.ac.uk.crt
SSLCertificateKeyFile /etc/pki/tls/certs/synthsys.inf.ed.ac.uk.key
SSLCertificateChainFile /etc/pki/tls/certs/synthsys.inf.ed.ac.uk.ca-bundle

Starting/stopping (Should be automatic on startup)

om apache start

om apache stop

om apache restart

Usergroup csbe-admin have access rights to do this.

BugZilla

Self-managed and self-contained BugZilla installation.

Accounts

See accounts sheet

Locations

/disk/data/web/html/bugs/

URLs

http://mook.inf.ed.ac.uk/bugs/

Matlab

Users SSH into the machine to run Matlab. Software itself is the standard DICE installation.

Licensing

Matlab - 10 licenses

BioInformatics Toolbox - 1

Curve Fitting Toolbox - 1

SimBiology - 2

Symbolic Math Toolbox - 1

Renewal due Feb-12

Licenses managed via Sheila, Graham and Tim.

URLs (user instructions)

http://homepages.inf.ed.ac.uk/sbarr2/csbe/matlab.html

phpMyAdmin

Accounts

Same login details as MySQL (user: root, password, same as tomcat/apache).

Locations

/disk/data/web/html/gengy

URLs

http://mook.inf.ed.ac.uk/gengy/

phpScheduleIt (CSBE Room Booking System)

Accounts

Alison & Tomasz have own accounts with admin access. support-team@infREMOVE_THIS.ed.ac.uk also has an account with standard password.

Locations

/disk/data/web/html/bookings/

URLs

http://mook.inf.ed.ac.uk/bookings/

http://mook.inf.ed.ac.uk/biosched/

Tomcat

Server has multiple tomcat installations and instances, a mix of managed and self-managed.

Users with csbe-admin role should be able to stop and start selfmanaged and their own instances of managed Tomcat. User account Tomcat has password set via LCFG profile.

Accounts

Linux system account (via LCFG):

See accounts sheet

Users (mainly tzielins) can do su tomcat and then run the startup/shutdown scripts.

Locations

The following instances are autostarted on boot:

BioDare :

/disk/data/tomcat/biodare/

Datamart:

/disk/data/tomcat/datamart/

FFT:

/disk/data/tomcat/fft/

Plasmo:

/disk/data/tomcat/plasmo/

SBSI:

/disk/data/tomcat/sbsi/

Tomcat6:

/disk/data/tomcat6/

The following instances are not:

/disk/data/managed_tomcat6/mhindle/prod and ./dev/

There may be others I'm not aware of.

Starting/stopping Tomcat (Should be automatic on boot - see LCFG profile for cron jobs)

su tomcat

/disk/data/tomcat/(sbsi|plasmo|biodare|fft|datamart)/bin/startup.sh

/disk/data/tomcat/(sbsi|plasmo|biodare|fft|datamart)/bin/shutdown.sh

Twiki

Centre wiki. Mainly used for order processing. Several users have admin role to manage user accounts, site layout, etc., though resetting passwords and deleting accounts are a complex process requiring nsu.

Google Removal

Users have specifically asked for the wiki to be removed from Google's index. This was previously requested for myself by Mook but may need to be repeated for the new alias synthsys.inf which has not been picked up yet

Attachments

TWiki by default makes all attachments publicly visible even if the page they are attached to is private. Users have requested this be overridden, so I have used the following workaround:

http://twiki.org/cgi-bin/view/TWiki/TWikiAccessControl#Securing_File_Attachments

This used to be implemented in the twiki.conf file but had to be moved to ssl.conf. The workaround basically implements user login control on attachments in the same way as wiki pages themselves. This is fine for users logged in but screws up attachments that should be publicly visible for users that don't have accounts (including embedded images).

Accounts

See accounts sheet

Locations

/disk/data/web/html/twiki/

URLs

http://synthsys.inf.ed.ac.uk/twiki

Topic revision: r2 - 06 Sep 2012 - 15:28:06 - YanHuang
 
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