CCLS CLIC

UC Berkeley, School of Public Health, California Childhood Leukemia Study

Childhood Leukemia International Consortium

Requirements

• ruby >= 2.1

• ImageMagick (which may require MacPorts)

  • ImageMagick is used to image manipulation

IMPORTANT NOTES

• For the time being, do not use apostrophes in the filenames of any uploaded files. I think that Paperclip does not deal with them, at least using expiring_url, and somehow the signature is incorrect.

• possible fix … www.davesouth.org/stories/make-url-friendly-filenames-in-paperclip-attachments

Installation

#	Copy secret_token file.
cp config/initializers/secret_token.rb.example config/initializers/secret_token.rb

#	Copy and setup database file.
cp config/database.yml.example config/database.yml

#	Copy and add your own gmail credentials.
cp config/initializers/mail.rb.example config/initializers/mail.rb

Possible For standard ruby users, install mysql gem …

#	If using mysql ...
# On Mac OS X:
#   sudo gem install mysql -- --with-mysql-dir=/usr/local/mysql
# On Mac OS X Leopard:
#   sudo env ARCHFLAGS="-arch i386" gem install mysql -- --with-mysql-config=/usr/local/mysql/bin/mysql_config
# ... I had to install the mysql gem like so ...

sudo env ARCHFLAGS="-arch x86_64" gem install mysql -- --with-mysql-config=/usr/local/mysql/bin/mysql_config

Everybody join hands together now to install some gems …

#
# Some gems require manual installation for one reason or another.
#
# (sudo may or may not be required or desired.
#  Usage of sudo will/may cause gem installation in /usr/lib
#  which may then require using sudo when running rake tasks
#  or other things.  `gem list` and `sudo gem list` will differ.
#  I recommend avoiding using sudo with rvm, but its your
#  kitchen.)
#
gem source -a http://gemcutter.org
gem source -a http://gems.github.com
sudo gem install bundler

# preferably use bundler to install all specific gem versions
sudo bundle install

then we continue …

#	Add your own session secret to config/initializers/secret_token.rb
#	generate a 128 character hex string perfect for using as your secret.
rake secret

rake db:migrate

#	add some expected items (loads fixtures OVERWRITING some db data)
rake app:setup

script/rails s

#	login to your app
#	The first administrator/deputy must be created via the command line.
#	Others can be created via the command line or web app.
#
rake app:deputize username=<Your Username>

#
#
#	The CLIC site no longer uses this functionality, but it has not been 
#	removed from the app.  Just the menu item.  Don't bother starting it.

# start sunspot:solr server (sunspot:solr:start does not work in jruby)
[jakewendt@ccls-01:~] > sudo su -l tomcat
[tomcat@ccls-01:~] > cd /var/lib/tomcat5/webapps/clic/WEB-INF
[tomcat@ccls-01:WEB-INF] > rake sunspot:solr:run RAILS_ENV=production &
# log MAY BE at /var/lib/tomcat5/webapps/clic/WEB-INF/log/sunspot-solr-production.log

Kenai

Berkeley Wiki

Documentation

Inline documentation is sparse and incomplete, but I’m working on it.

sudo gem install rdoc --source http://gemcutter.org
rake doc:plugins
rake doc:app
open doc/app/README_rdoc.html

Further Info

Ruby Best Practices

RVM on GitHub

To Do

• Fix expire_fragment "#{request.try(:host_with_port)}#{page_path}" so that it works without the try (not necessary)

• Add to doc/README_FOR_APP

• one of the images in rdoc isn’t always the correct directory depth and will create a flash error showing this

Credit / Special Thanks

Gradient images made with Gradient Image Maker

Demo on css rounded corners

Background image gradients

SQLite3 to MySQL

sqlite3 clic.sqlite3.20110809 .dump > clic.sqlite3.20110809.dump

Edit the dump file and remove all lines like …

PRAGMA foreign_keys=OFF;
BEGIN TRANSACTION;
CREATE TABLE ....
INSERT INTO "schema_migrations" ...
DELETE FROM sqlite_sequence;
INSERT INTO "sqlite_sequence" ....
CREATE UNIQUE INDEX ....
CREATE INDEX ....
COMMIT;

Convert table name quotes from double quotes to backticks in vim with …

%s/INSERT INTO "/INSERT INTO `/
%s/" VALUES(/` VALUES(/

Import to mysql database

rake db:migrate RAILS_ENV=production
mysql -u magee -p --host=cascades.ist.berkeley.edu --port=3347 CCLS_Systems < clic.sqlite3.20110809.dump.forimport

The boolean values did not export/import well, but none were terribly important. This should be noted if ever doing this again with boolean values that do matter.

Other

Forking is frowned upon in jruby so using “start” won’t work.

To start the solr server just “run” it in the background. Can’t seem to get a “commit” to work in production so need to build the index elsewhere and import everything. Not gonna work in the long term. Also has a tendency to crash out silently.

rake sunspot:solr:run &
cp ~jakewendt/CCLS_Aust_Covariate_sample.csv ./
rake app:subjects:import --trace
rake "sunspot:reindex" --trace

---

Date.today

DO NOT USE Date.today, unless the following is what you want.

It will compute a Date and disregard the time zone.

In rails, this means that occassionally Date.today == Date.tomorrow or Date.today == Date.yesterday, depending on what time it is.

The Rails methods of Date.tomorrow and Date.yesterday reference Date.current, which uses the Time.zone, making them more accurate.

I think that DateTime.now and Time.now also ignore the timezone.

Use DateTime.current or Time.zone.now

---

Quick Development Notes

c ; /bin/rm -rf coverage* ; bundle exec rake ; mv coverage coverage-one-run ; open coverage-one-run/index.html ; nice +20 bundle exec autotest -v --no-full-after-failed

---

Quick Production Notes

Unfortunately, killing the server could result in lost data that may be cached in memory. At least in theory. I don’t think that rails really caches like that.

CLIC IS ON PORT 3001 !!!!

cd /my/ruby/clic
kill -9 `cat tmp/pids/server.pid`
git pull
bundle install
rake db:migrate
script/rails server -d -p 3001 -e production

FYI web admin pings this site every 5-10 seconds which will make the log pretty big.