Latticegrid scripts

# useful plugins

# documentation: http://cardboardrocket.com/pages/paginating_find

#no longer using this (5/5/2008)

#script/plugin install http://svn.cardboardrocket.com/paginating_find

# documentation: http://bparanj.blogspot.com/2007/09/how-to-use-will-paginate-20-rails.html

# documentation: http://errtheblog.com/posts/56-im-paginating-again

# replaced with mislav-will-paginate gem

#script/plugin install svn://errtheblog.com/svn/plugins/will_paginate

#ldap stuff

# may need to register this site: http://rubyforge.org/projects/net-ldap/

 sudo gem install ruby-net-ldap

# sparklines

 sudo gem install sparklines
 sudo gem install sparklines_generator

# may need to do this too:

 sudo gem install rmagick
 ruby script/generate sparklines

# for sparklines, add to bottom of config/environment.rb

 require 'sparklines'

# in the controller where you want to use a sparkline:

#class MyController < ApplicationController

 helper :sparklines

# call in any view for that controller:

<%= sparkline_tag [10,20,30], :type => 'pie' %>

#csv parser

 sudo gem install fastercsv

#simple date select plugin

 script/plugin install svn://code.jeremyevans.net/rails/plugins/simple_date_select

# acts_as_taggable

 script/plugin install http://svn.viney.net.nz/things/rails/plugins/acts_as_taggable_on_steroids
 --PostgreSQL commands
 -- add this line to pg_hba.conf so you can connect to it on the local machine without a password, if you so desire
 local  all    cancerpublications   trust
 -- now login to postgres using psql
 psql postgres
 -- create the user (role)
 -- for a little bit of security, create a role. user is an alias for role that also specifies that the role is permitted to login
 CREATE USER cancerpublications with createdb;

#if you need to add the createdb role to user, do it like this:

 ALTER USER cancerpublications with createdb;

 -- you can also specify a user and password:
 CREATE USER nucatspublications WITH PASSWORD 'jw8s0F4';
 -- or if the user has already been created:
 ALTER USER nucatspublications WITH PASSWORD 'jw8s0F4';

 -- or add a end date to the user:
 CREATE ROLE nucatspublications WITH LOGIN PASSWORD 'jw8s0F4' VALID UNTIL '2008-01-01';

 -- now switch to the new user
 \connect - cancerpublications

 -- now create the database
 create database cancerpublications_development;
 create database cancerpublications_test;
 create database cancerpublications_production;

# You can also use the shell script but this requires looser security, specifying access, or reassigning ownership of the database

 createdb cancerpublications_development
 createdb cancerpublications_test
 -- and specify privileges if you did not create the database using the new user. Skip this step if you used the new user
 GRANT SELECT, INSERT, UPDATE ON TABLE schema_info TO nucatspublications;

 -- sequences
 GRANT SELECT, UPDATE ON  allele_types_id_seq, animal_model_publications_id_seq, animal_models_id_seq, model_types_id_seq, mutation_methods_id_seq, pi_contacts_id_seq,  tumor_types_id_seq TO animalmodels;

# create rails app

 rails -d postgresql cancerpublications
 cd nucatspublications
 bbedit config/database.yml

#make sure you have a section that looks like:

 development:
   adapter: postgresql
   database: cancerpublications_development
   username: cancerpublications
 test:
   adapter: postgresql
   database: cancerpublications_test
   username: cancerpublications

# create the controller

  script/generate controller abstracts
        script/generate controller graphs
        script/generate controller programs
        script/generate controller investigators

# create Models

# now create a model

  script/generate model abstract
        script/generate model investigator
        script/generate model investigator_abstract
        script/generate model program
        script/generate model program_abstract
        script/generate model investigator_program
        script/generate model proposal
        script/generate model investigator_proposal
        script/generate model study
        script/generate model investigator_study
        script/generate model investigator_relationship

# for graphing the connections

  script/generate controller graph
        script/generate model graph

# edit the db/migrate script

 bbedit db/migrate/001_create_abstracts.rb
 bbedit db/migrate/002_create_investigators.rb
 bbedit db/migrate/003_create_investigator_abstracts.rb
 bbedit db/migrate/004_create_programs.rb
 bbedit db/migrate/005_create_investigator_programs.rb

# create the scaffolds

  script/generate scaffold abstract

# after changing the table create script to create the necessary features, try it with rake:

# test that the models can be generated and moved

     rake db:migrate

# reverse the migration

    rake db:migrate VERSION=0

# repeat

     rake db:migrate

# do it in production:

 rake environment RAILS_ENV=production db:migrate

# do it in test:

 rake environment RAILS_ENV=test db:migrate

# install additional investigators using ldap

 rake getLDAP uid_list=aqw,wakibbe

#RUN TESTS

 ruby test/unit/abstract_test.rb

# clean all usernames by removing any periods

 rake cleanInvestigatorsUsername

# load data using the insertAbstracts rake task

 rake insertAbstracts
 rake RAILS_ENV=production insertAbstracts

#insert all abstracts (10 years)

 rake insertAllAbstracts
 rake RAILS_ENV=production insertAllAbstracts

#update member associations based on loaded publications

 rake associateAbstractsWithInvestigators
 rake RAILS_ENV=production associateAbstractsWithInvestigators

# update publication information like first and last authors

 rake updateAbstractInvestigators

#update publication information for each investigator, include collaboration information

 rake updateInvestigatorInformation

#create tags from MeSH data for each abstract

 rake tagAbstractsWithMeshTerms

#create tags from MeSH data for each investigator

# runs in 25 minutes

 tagInvestigatorsWithMeshTerms

#update publication information for each program

 rake updateProgramAbstractInformation

#all the expected tasks are run using this build command

# runs these tasks: :insertAbstracts, :associateAbstractsWithInvestigators, :updateAbstractInvestigators, :updateInvestigatorInformation, :tagAbstractsWithMeshTerms, :updateProgramAbstractInformation

 rake nightlyBuild
 rake RAILS_ENV=production nightlyBuild

# something to do weekly is:

 vacuumdb -fz cancerpublications_development

#all the mesh associations are run with this command

 rake monthlyBuild
 rake RAILS_ENV=production monthlyBuild

# see file generateGraphs.sh for how to generat connection graphs for cancer center member publications

#start web server

     script/server

# clear logs

 rake log:clear

# passenger restart

 touch tmp/restart.txt

# some quality control sql to run

 select count(*) from abstracts where year is null;
 select count(*) from abstracts where publication_date is null;
 select count(*) from abstracts where electronic_publication_date is null;
 select count(*), year from abstracts  group by year order by year;
 select count(*), year from abstracts where publication_date is null group by year order by year;
 select count(*), year from abstracts where electronic_publication_date is null group by year order by year;
 select count(*), year from abstracts where electronic_publication_date > publication_date  group by year order by year;