Telomere Length Recording Application HowTo Install

Tags: Telomere Length Recording Application HowTo Install Pain in the proverbial UoL LAMP Server

See: UoL LAMP HowTo Install Python Flask Applications

Requirements

Before installation can start, the following packages will have to be installed by IT services:

• libmysqlclient-dev
• python-dev
• libldap2-dev
• libsasl2-dev

Difficulties

This installations is made more difficult by 3 things:

1. Suse Linux does not have mod_wsgi in its repositories, so you're going to have to compile it.
2. mod_wsgi seems picky about where it picks python apps and libraries from
3. The LAMP servers don't put things where you'd expect them to be.
4. Some other stuff that I don't quite understand

Start Services

Start the Apache and MySQL and make sure that they are restarted when the server is rebooted.

sudo /sbin/chkconfig uol.apache2 on
sudo /etc/init.d/uol.apache2 start
sudo /sbin/chkconfig uol.mysql on
sudo /etc/init.d/uol.mysql start

Proceduce

1. HowTo Compile mod_wsgi for LAMP servers
2. Copy the Telomere application from the git repository into /local/ directory.
3. Install virtualenv:

easy_install --install-dir=/local/python virtualenv

For some reason that I can't work out (point 4. above), it would only pick up some of the python libraries from a virtual env and not when they were installed in /local/python/. Maybe this was because of the order that I installed things, but I couldn't get it to work without the virtual environment.

4. Create a virtual environment in the telomere application directory.

cd /local/telomere
/local/python/virtualenv --no-site-packages BASELINE

BASELINE is the name of the virtual environment. It could be called anything, but it's called that! Also note that you need to use the full path to the virtualenv utility, since /local/python isn't in $PATH.

5. Activate the environment, install the required packages, then deactivate:

source BASELINE/bin/activate
easy_install flask
easy_install flask-sqlalchemy
easy_install mysql-python
easy_install flask-login
easy_install python-ldap
easy_install flask-wtf
easy_install WTForms-Components
easy_install openpyxl
deactivate

6. Load the WSGI module into Apache, by editing the file /local/apache2/etc/loadmodule.conf by adding this line at the end.

LoadModule wsgi_module /local/apache2/etc/mod_wsgi.so

This presumes that you've copied the compiled mod_wsgi.so file into the /local/apache2/etc/ directory.

7. Add the WSGI config to the Apache config file /local/apache2/etc/httpd.conf:

<Directory /local/telomere>
    WSGIProcessGroup telomere
    WSGIApplicationGroup %{GLOBAL}
    Order deny,allow
    Allow from all
</Directory>

WSGIDaemonProcess telomere user=wwwrun threads=5 python-path=/local/telomere/BASELINE/lib/python2.6/site-packages:/local/python:/usr/lib64/python2.6/site-packages:/usr/share/doc/packages/ home=/local/telomere/
WSGIScriptAlias / /local/telomere/app/telomere.wsgi

The two hard won things here are the values for the python-path and home arguments. The python-path must contain every directory where python libraries are installed, including a sub-directory of the virtualenv directory you created earlier. The home must point to your application directory, or you won't be able to pick up your own modules.

8. Restart apache:

sudo /etc/init.d/uol.apache2 restart

9. Pray.

Other Possible Stuff

1. You may need to give wwwrun extra permissions to the /local/telomere directory.
2. You might need to pray a bit more.

Permission to Upload Directory

1. In order to upload spreadsheets, you need to create an upload directory, for example /local/telomere/uploads.
2. You then need to point to this in the settings.py file SPREADSHEET_UPLOAD_DIRECTORY = '/local/telomere/uploads'
3. Finally, you need to give wwwrun permission to read and write to the directory.

setfacl -m u:wwwrun:rwx /local/telomere/uploads/
setfacl -m d:u:wwwrun:rwx /local/telomere/uploads/

Error: Macro BackLinks(None) failed

'Environment' object has no attribute 'get_db_cnx'