danmaclean

	I, the reviewer, promise:
  	1. to not hide behind a screen of anonymity
 	2. to be open and honest with you (the authors) at all times
	3. to be constructive in my criticism
 	4. within the rules given to me by the journal, to assist you in every way I ethically can to get your manuscript published,by providing criticism and praise that is valid and relevant
 	
 	
 	Dan MacLean
 	The Sainsbury Laboratory

danmaclean

## The Reviewer

I, the reviewer, promise:
	1. to not hide behind a screen of anonymity
	2. to be open and honest with you (the authors) at all times
	3. to be constructive in my criticism
	4. within the rules given to me by the journal, to assist you in every way I ethically can to get your manuscript published,by providing criticism and praise that is valid and relevant
	5. It is your paper, not mine. I will not try to turn author’s paper into a paper I would have written.
	
	

danmaclean

irb(main):001:0> require 'bio'
=> true
irb(main):002:0> r = Bio::GFF::GFF3.new()
=> #<Bio::GFF::GFF3:0x007ff22b911ea8 @gff_version=nil, @records=[], @sequence_regions=[], @metadata=[], @sequences=[], @in_fasta=false>
irb(main):003:0> r = Bio::GFF::GFF3::Record.new()
=> #<Bio::GFF::GFF3::Record:0x007ff22c104728 @seqname=nil, @source=nil, @feature=nil, @score=nil, @strand=nil, @attributes=[], @start=nil, @end=nil, @frame=nil>
irb(main):004:0> r.seqname = "meh"
=> "meh"
irb(main):005:0> r
=> #<Bio::GFF::GFF3::Record:0x007ff22c104728 @seqname="meh", @source=nil, @feature=nil, @score=nil, @strand=nil, @attributes=[], @start=nil, @end=nil, @frame=nil>

danmaclean

$ biogem --with-engine Foo foo
$ cd bioruby-foo
$ rake version:write
update gemfile to specify new version of bundler
$ bundle install
Note: a database is automatically configure for the newly created gem
$ cd ../
$ rails new Webfoo
$ add `gem 'bio-foo', :path=>'path_gem_dir' `  into Rails application Gemfile the newly created gem:
$ cd Webfoo

danmaclean

require 'rubygems'
require 'json'


require 'rack'
require 'rinruby'

class HelloApp
  def call(env)
    req = Rack::Request.new(env)

danmaclean

ActiveModel::MassAssignmentSecurity::Error in ExperimentsController#create

Can't mass-assign protected attributes: yaml_file
Rails.root: /Users/macleand/Downloads/gee_fu-experimental-8

Application Trace | Framework Trace | Full Trace
activemodel (3.2.13) lib/active_model/mass_assignment_security/sanitizer.rb:48:in `process_removed_attributes'
activemodel (3.2.13) lib/active_model/mass_assignment_security/sanitizer.rb:20:in `debug_protected_attribute_removal'
activemodel (3.2.13) lib/active_model/mass_assignment_security/sanitizer.rb:12:in `sanitize'
activemodel (3.2.13) lib/active_model/mass_assignment_security.rb:230:in `sanitize_for_mass_assignment'

danmaclean

rake repo:export
DEPRECATION WARNING: You have Rails 2.3-style plugins in vendor/plugins! Support for these plugins will be removed in Rails 4.0. Move them out and bundle them in your Gemfile, or fold them in to your app as lib/myplugin/* and config/initializers/myplugin.rb. See the release notes for more on this: http://weblog.rubyonrails.org/2012/1/4/rails-3-2-0-rc2-has-been-released. (called from <top (required)> at /Users/macleand/Downloads/gee_fu-experimental-8/Rakefile:7)
rake aborted!
Couldn't find Reference without an ID
/Users/macleand/.rvm/gems/ruby-1.9.3-p286@gee_fu/gems/activerecord-3.2.13/lib/active_record/relation/finder_methods.rb:312:in `find_with_ids'
/Users/macleand/.rvm/gems/ruby-1.9.3-p286@gee_fu/gems/activerecord-3.2.13/lib/active_record/relation/finder_methods.rb:107:in `find'
/Users/macleand/.rvm/gems/ruby-1.9.3-p286@gee_fu/gems/activerecord-3.2.13/lib/active_record/querying.rb:5:in `find'
/Users/macleand/Downloads/gee_fu-experimental-8/app/models/feature.rb:225:in `to_gff'
/Users/macle

danmaclean

macleand$ foreman s
15:43:33 web.1    | started with pid 36997
15:43:33 worker.1 | started with pid 36998
15:43:36 worker.1 | DEPRECATION WARNING: You have Rails 2.3-style plugins in vendor/plugins! Support for these plugins will be removed in Rails 4.0. Move them out and bundle them in your Gemfile, or fold them in to your app as lib/myplugin/* and config/initializers/myplugin.rb. See the release notes for more on this: http://weblog.rubyonrails.org/2012/1/4/rails-3-2-0-rc2-has-been-released. (called from <top (required)> at /Users/macleand/Downloads/gee_fu-experimental-8/config/environment.rb:5)
15:43:36 web.1    | DEPRECATION WARNING: You have Rails 2.3-style plugins in vendor/plugins! Support for these plugins will be removed in Rails 4.0. Move them out and bundle them in your Gemfile, or fold them in to your app as lib/myplugin/* and config/initializers/myplugin.rb. See the release notes for more on this: http://weblog.rubyonrails.org/2012/1/4/rails-3-2-0-rc2-has-been-released. (called from <top (require

danmaclean

      File.open( "#{@experiment.gff_file.path}" ).each do |line|
        next if line =~ /^#/
        break if line =~ /^##fasta/ or line =~ /^>/
        record = Bio::GFF::GFF3::Record.new(line)

danmaclean

        ref = Reference.find(:first, :conditions => ["name = ? AND genome_id = ?", "#{ record.seqname }", "#{@experiment.genome_id}"])

        feature = Feature.new(
          :group => "#{attribute}",
          :feature => "#{record.feature}",
          :source => "#{record.source}",
          :start => "#{record.start}",
          :end => "#{record.end}", 
          :strand => "#{record.strand}",
          :phase => "#{record.frame}",