active_unimod_generator 0.1.0

data/History

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+== 0.1.0 / 2007-12-20 revision 16
+
+Initial release with all Unimod tables represented as 
+ActiveRecord models.  Includes: 
+
+* a generator for creating the ActiveUnimod models
+  within a Rails app
+* migrations to create a local Unimod database
+* tasks for creating/updating the local database

data/MIT-LICENSE

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+Copyright (c) 2006-2007, Regents of the University of Colorado.
+Developer:: Simon Chiang, Biomolecular Structure Program, Hansen Lab
+Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this
+software and associated documentation files (the "Software"), to deal in the Software
+without restriction, including without limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
+to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or
+substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/README

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+= ActiveUnimod
+
+ActiveRecord models for the {Unimod}[http://www.unimod.org] database.
+
+== Description
+
+ActiveUnimod is a generator gem containing ActiveRecord models and database migrations 
+to setup and utilize the Unimod database.  The ActiveUnimod models implement associations 
+as documented in the {unimod schema}[http://www.unimod.org/pdf/unimod_schema.pdf].
+
+ActiveUnimod is a part of the BioActive[http://rubyforge.org/projects/bioactive] project
+and is not a part of Unimod itself.
+
+=== Features/Problems
+
+- ActiveUnimod can be used to generate models within a rails project, or programatically as a gem.
+- ActiveUnimod includes tasks to update a local database using the web-available {data}[http://www.unimod.org/xml/unimod_tables.xml].
+- Several associations could not be implemented cleanly because they join tables based
+  on fields other than the primary key.  (ex: the associations based on bricks.brick)
+
+== Installation
+
+ActiveUnimod is available as a gem on RubyForge[http://rubyforge.org/projects/bioactive].  Use:
+
+  % gem install active_unimod_generator
+  
+== Generator Usage
+
+Use like any other generator gem:
+
+  % script/generate active_unimod
+
+Migrate in the Unimod tables as normal:
+
+  % rake db:migrate
+  
+Update the data in the database:
+
+  % rake active_unimod:database:update
+
+== Usage
+
+  require 'active_unimod'
+  
+  # establish a connection... for instance using sqlite (see below)
+  ActiveRecord::Base.establish_connection(
+    :adapter => 'sqlite3',
+    :database => 'unimod')
+    
+  # update the database if needed
+  require 'active_unimod/database'
+  ActiveUnimod::Database.create_tables
+  ActiveUnimod::Database.update_from_web
+  
+  # now use the models
+  Classification.find_by_classification("Other glycosylation").modifications.collect do |m| 
+    m.full_name
+  end.uniq
+  
+  # => ["Hexose",
+  #        "N-Acetylhexosamine",
+  #        "N-acetylglucosamine-1-phosphoryl",
+  #        "phosphoglycosyl-D-mannose-1-phosphoryl",
+  #        "ADP  Ribose addition",
+  #        "Lactosylation",
+  #        "propyl-1,2-dideoxy-2\\'-methyl-alpha-D-glucopyranoso-[2,1-d]-Delta2\\'-thiazoline"]
+  
+== Info 
+
+Copyright (c) 2006-2007, Regents of the University of Colorado.
+Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/] 
+Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
+Licence:: MIT-Style
+
+== SQLite installation
+
+ActiveRecord can connect to a wide variety of databases. SQLite is used
+in the examples because it is the easiest to get running.  Here are the 
+basic installation instructions.  
+
+=== Install the binaries
+
+On Mac OSX/Unix, sqlite3 is usually pre-installed.  Try calling sqlite3 
+from a command prompt to check (see below).  If it isn't installed, check the 
+{sqlite website}[http://www.sqlite.org/] for installation instructions.  
+
+On Windows:
+# Download the sqlite3 command line program and .dll from the 
+  {downloads page}[http://www.sqlite.org/download.html].  They 
+   will be named like sqlite-3_version.zip and sqlitedll-3_version.zip 
+   respectively.
+# Extract/copy these files (sqlite3.exe and sqlite3.dll) into C:\ruby\bin, 
+   or the bin directory of wherever you installed ruby.
+  
+Now you should be able to access sqlite3 from a command prompt:
+
+  % sqlite3
+  SQLite version 3.[version]
+  Enter ".help" for instructions
+  sqlite> 
+  
+=== Install the ruby bindings
+
+  % gem install sqlite3-ruby
+
+And that's it!  

data/Rakefile

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+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require(File.join(File.dirname(__FILE__), 'config', 'boot'))
+
+require 'rake'
+require 'rake/testtask'
+require 'rake/rdoctask'
+
+require 'tasks/rails'
+require 'rake/gempackagetask'
+require 'active_unimod_tasks'
+
+#
+# Gem specification
+#
+Gem::manage_gems
+spec = Gem::Specification.new do |s|
+	s.name = "active_unimod_generator"
+	s.version = "0.1.0"
+	s.author = "Simon Chiang"
+	s.email = "simon.chiang@uchsc.edu"
+	s.homepage = "http://rubyforge.org/projects/bioactive/active_unimod"
+	s.platform = Gem::Platform::RUBY
+	s.summary = "ActiveRecord models and database migrations for Unimod."
+	s.files = Dir.glob("app/models/*") + Dir.glob("{db,lib}/**/*") + ["Rakefile", "active_unimod_generator.rb"]
+	s.autorequire = "active_unimod"
+	#s.test_file = "test/active_unimod_test_suite.rb"
+	
+	s.has_rdoc = true
+	s.extra_rdoc_files = ["README", "MIT-LICENSE", "History"]
+  s.rdoc_options << '--title' << 'ActiveUnimod' << '--main' << 'README' 
+	s.add_dependency("activerecord", ">= 2.0.1")
+  s.add_dependency("hpricot", ">= 0.6.0")
+end
+
+pkg = Rake::GemPackageTask.new(spec) do |pkg|
+	pkg.need_tar = true
+end
+
+#
+# documentation tasks
+#
+
+desc 'Generate documentation.'
+Rake::RDocTask.new(:rdoc) do |rdoc|
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title    = 'Active Unimod'
+  rdoc.main = 'README'
+  rdoc.options << '--line-numbers' << '--inline-source'
+  rdoc.rdoc_files.concat spec.files.select {|file| File.file?(file) && file !~ /templates|Rakefile/ }
+end
+
+#
+# hoe tasks
+#
+
+desc "Publish RDoc to RubyForge"
+task :publish_rdoc => [:rdoc] do
+  require 'yaml'
+  
+  config = YAML.load(File.read(File.expand_path("~/.rubyforge/user-config.yml")))
+  host = "#{config["username"]}@rubyforge.org"
+  
+  rsync_args = "-v -c -r"
+  remote_dir = "/var/www/gforge-projects/bioactive/active_unimod_generator"
+  local_dir = "rdoc"
+ 
+  sh %{rsync #{rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
+end

data/active_unimod_generator.rb

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+require File.dirname(__FILE__) + '/lib/generators/active_unimod/active_unimod_generator.rb'
+
+# Gem Generators require the generator to be available from
+# a 'generators' or 'rails_generators' path, or a '_generator.rb' 
+# file within the gem.  Like so:
+#
+#   gems/gem_generator-0.1.0/gem_generator.rb
+#
+# By contrast the natural place to develop a gem is within the 
+# 'lib/generators' directory.  When the gem generaator is loaded
+# it recieves a spec that defines the path where the generator
+# was found, and that path is used to discover templates, etc.
+#
+# This module redirects the path to the natural packaging location
+# for the generator.
+module RedirectSpecPath # :nodoc:
+  def spec=(spec)
+    if spec.source == :RubyGems
+      spec.instance_variable_set("@path",  File.join(spec.path, "/lib/generators/active_unimod"))
+    end
+    super
+  end
+end
+
+ActiveUnimodGenerator.extend RedirectSpecPath

data/app/models/alt_name.rb

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+class AltName < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  belongs_to :modification, :foreign_key => 'mod_key'
+end

data/app/models/amino_acid.rb

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+class AminoAcid < ActiveRecord::Base
+  self.primary_key = "record_id"
+end

data/app/models/brick.rb

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+class Brick < ActiveRecord::Base
+  self.primary_key = "record_id"
+end

data/app/models/brick2element.rb

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+class Brick2element < ActiveRecord::Base
+  set_table_name "brick2element"
+  self.primary_key = "record_id"
+end

data/app/models/classification.rb

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+class Classification < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  has_many :specificities, :foreign_key => 'classifications_key'
+  has_many :modifications, :through => :specificities
+end

data/app/models/element.rb

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+class Element < ActiveRecord::Base
+  self.primary_key = "record_id"
+end

data/app/models/fragment.rb

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+class Fragment < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  has_many :fragment_comps, :foreign_key => 'fragments_key'
+  belongs_to :modification, :foreign_key => 'mod_key'
+end

data/app/models/fragment_comp.rb

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+class FragmentComp < ActiveRecord::Base
+  set_table_name "fragment_comp"
+  self.primary_key = "record_id"
+  
+  belongs_to :fragment, :foreign_key => 'fragments_key'
+end

data/app/models/log.rb

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+class Log < ActiveRecord::Base
+  set_table_name "log"
+  self.primary_key = "record_id"
+end

data/app/models/mod2brick.rb

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+class Mod2brick < ActiveRecord::Base
+  set_table_name "mod2brick"
+  self.primary_key = "record_id"
+  
+  belongs_to :modification, :foreign_key => 'mod_key'
+end

data/app/models/modification.rb

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+class Modification < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  has_many :fragments, :foreign_key => 'mod_key'
+  has_many :alt_names, :foreign_key => 'mod_key'
+  
+  has_many :xrefs, :foreign_key => 'mod_key'
+  has_many :xref_sources, :through => :xrefs
+  
+  has_many :mod2bricks, :foreign_key => 'mod_key'
+  
+  has_many :specificities, :foreign_key => 'mod_key'
+  has_many :positions, :through => :specificities
+  has_many :classifications, :through => :specificities
+
+end

data/app/models/neutral_loss.rb

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+class NeutralLoss < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  belongs_to :spec2nl, :foreign_key => 'spec_key'
+end

data/app/models/position.rb

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+class Position < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  has_many :specificities, :foreign_key => 'position_key'
+  has_many :modifications, :through => :specificities
+end

data/app/models/spec2nl.rb

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+class Spec2nl < ActiveRecord::Base
+  set_table_name "spec2nl"
+  self.primary_key = "record_id"
+  
+  belongs_to :specificity, :foreign_key => 'spec_key'
+  has_many :neutral_losses, :foreign_key => 'spec_key'
+end

data/app/models/specificity.rb

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+class Specificity < ActiveRecord::Base
+  set_table_name "specificity"
+  self.primary_key = "record_id"
+  
+  has_many :spec2nls, :foreign_key => 'spec_key'
+  belongs_to :modification, :foreign_key => 'mod_key'
+  belongs_to :position, :foreign_key => 'position_key'
+  belongs_to :classification, :foreign_key => 'classifications_key'
+end

data/app/models/user.rb

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+class User < ActiveRecord::Base
+  self.primary_key = "record_id"
+end

data/app/models/xref.rb

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+class Xref < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  belongs_to :modification, :foreign_key => 'mod_key'
+  belongs_to :xref_source, :foreign_key => 'xref_source_key'
+end

data/app/models/xref_source.rb

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+class XrefSource < ActiveRecord::Base
+  self.primary_key = "record_id"
+  
+  has_many :xrefs, :foreign_key => 'xref_source_key'
+  has_many :modifications, :through => :xrefs
+end

data/db/migrate/001_active_unimod_schema.rb

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+# == Field Definition
+#
+# The official Unimod database is a MYSQL database and uses several
+# MYSQL-specific field definitions such as:
+#
+#  `mono_mass` double NOT NULL default '0',
+#  `mono_mass` double(12,6) default NULL,
+#
+# Doubles are normally treated as floats in the database-independent
+# definitions of migrations.  This is not sufficient for several Unimod
+# fields (ex mono_mass and avge_mass).  When possible I've defined
+# the doubles as decimals using the specified precision and scale; when
+# no precision and scale are specified (as in elements) I picked values
+# capable of handling the inputs from: 
+# http://www.unimod.org/xml/unimod_tables.xml
+#
+# == Indicies
+#
+# Unimod has a number of indicies which are all omitted in this
+# migration, because a number of them have conflicting names
+# that are not ok with SQLite.  This may affect performance
+# negatively, but portablility positively.  
+#
+
+class ActiveUnimodSchema < ActiveRecord::Migration
+  def self.up
+
+  create_table "alt_names", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",  :default => 0,  :null => false
+    t.string  "alt_name", :default => "", :null => false
+  end
+
+  create_table "amino_acids", :primary_key => "record_id", :force => true do |t|
+    t.string  "one_letter",                :default => "", :null => false
+    t.string  "three_letter"
+    t.string  "full_name"
+    t.integer "num_H",        :limit => 6, :default => 0
+    t.integer "num_C",        :limit => 6, :default => 0
+    t.integer "num_N",        :limit => 6, :default => 0
+    t.integer "num_O",        :limit => 6, :default => 0
+    t.integer "num_S",        :limit => 6, :default => 0
+  end
+
+  create_table "brick2element", :primary_key => "record_id", :force => true do |t|
+    t.integer "brick_key",                :default => 0,  :null => false
+    t.string  "element",                  :default => "", :null => false
+    t.integer "num_element", :limit => 6, :default => 1
+  end
+
+  create_table "bricks", :primary_key => "record_id", :force => true do |t|
+    t.string "brick",     :default => "", :null => false
+    t.string "full_name"
+  end
+
+  create_table "classifications", :primary_key => "record_id", :force => true do |t|
+    t.string "classification", :default => "", :null => false
+  end
+
+  create_table "elements", :primary_key => "record_id", :force => true do |t|
+    t.string "element",   :default => "",  :null => false
+    t.string "full_name"
+    t.decimal  "mono_mass", :precision => 12, :scale => 9, :default => 0.0, :null => false
+    t.decimal  "avge_mass", :precision => 12, :scale => 9, :default => 0.0, :null => false
+  end
+
+  create_table "fragment_comp", :primary_key => "record_id", :force => true do |t|
+    t.integer "fragments_key",              :default => 0,  :null => false
+    t.string  "brick",                      :default => "", :null => false
+    t.integer "num_brick",     :limit => 6, :default => 1
+  end
+
+  create_table "fragments", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key", :default => 0, :null => false
+  end
+
+  create_table "log", :primary_key => "record_id", :force => true do |t|
+    t.datetime "timestamp", :null => false
+    t.text     "query"
+  end
+
+  create_table "mod2brick", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",                :default => 0,  :null => false
+    t.string  "brick",                  :default => "", :null => false
+    t.integer "num_brick", :limit => 6, :default => 1
+  end
+
+  create_table "modifications", :primary_key => "record_id", :force => true do |t|
+    t.string   "full_name",                        :default => "", :null => false
+    t.string   "code_name",                        :default => "", :null => false
+    t.decimal    "mono_mass",          :precision => 12, :scale => 6
+    t.decimal    "avge_mass",          :precision => 12, :scale => 4
+    t.string   "composition"
+    t.text     "misc_notes"
+    t.string   "username_of_poster",               :default => "", :null => false
+    t.string   "group_of_poster",                  :default => "", :null => false
+    t.datetime "date_time_posted",                                 :null => false
+    t.datetime "date_time_modified",                               :null => false
+    t.string   "ex_code_name"
+    t.integer  "approved",           :limit => 4,  :default => 0
+  end
+
+  create_table "neutral_losses", :primary_key => "record_id", :force => true do |t|
+    t.integer "spec_key",               :default => 0,  :null => false
+    t.string  "brick",                  :default => "", :null => false
+    t.integer "num_brick", :limit => 6, :default => 1
+  end
+
+  create_table "positions", :primary_key => "record_id", :force => true do |t|
+    t.string "position", :default => "", :null => false
+  end
+
+  create_table "spec2nl", :primary_key => "record_id", :force => true do |t|
+    t.integer "spec_key",                     :default => 0, :null => false
+    t.integer "is_pep_nl",      :limit => 4,  :default => 0
+    t.integer "is_req_pep_nl",  :limit => 4,  :default => 0
+    t.integer "is_slave_nl",    :limit => 4,  :default => 0
+    t.decimal   "nl_mono_mass",   :precision => 12, :scale => 6
+    t.decimal   "nl_avge_mass",   :precision => 12, :scale => 4
+    t.string  "nl_composition"
+  end
+
+  create_table "specificity", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",                          :default => 0,  :null => false
+    t.string  "one_letter",                       :default => "", :null => false
+    t.integer "position_key",                     :default => 0,  :null => false
+    t.integer "hidden",              :limit => 4, :default => 0
+    t.integer "spec_group",          :limit => 6, :default => 0
+    t.integer "classifications_key",              :default => 0,  :null => false
+    t.text    "misc_notes"
+  end
+
+  create_table "users", :primary_key => "record_id", :force => true do |t|
+    t.string "UserName", :limit => 64
+    t.string "Password", :limit => 64
+    t.string "GroupID",  :limit => 64
+    t.string "FullName"
+    t.string "Email"
+  end
+
+  create_table "xref_sources", :primary_key => "record_id", :force => true do |t|
+    t.string "xref_source", :default => "", :null => false
+  end
+
+  create_table "xrefs", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",         :default => 0, :null => false
+    t.integer "xref_source_key", :default => 0, :null => false
+    t.text    "xref_text"
+    t.string  "xref_url"
+  end
+
+  end
+
+  def self.down
+    drop_table :alt_names
+    drop_table :amino_acids
+    drop_table :brick2element
+    drop_table :bricks
+    drop_table :classifications
+    drop_table :elements
+    drop_table :fragment_comp
+    drop_table :fragments
+    drop_table :log
+    drop_table :mod2brick
+    drop_table :modifications
+    drop_table :neutral_losses
+    drop_table :positions
+    drop_table :spec2nl
+    drop_table :specificity
+    drop_table :users
+    drop_table :xref_sources
+    drop_table :xrefs
+  end
+end

data/db/schema.rb

@@ -0,0 +1,142 @@
+# This file is auto-generated from the current state of the database. Instead of editing this file, 
+# please use the migrations feature of ActiveRecord to incrementally modify your database, and
+# then regenerate this schema definition.
+#
+# Note that this schema.rb definition is the authoritative source for your database schema. If you need
+# to create the application database on another system, you should be using db:schema:load, not running
+# all the migrations from scratch. The latter is a flawed and unsustainable approach (the more migrations
+# you'll amass, the slower it'll run and the greater likelihood for issues).
+#
+# It's strongly recommended to check this file into your version control system.
+
+ActiveRecord::Schema.define(:version => 1) do
+
+  create_table "alt_names", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",  :default => 0,  :null => false
+    t.string  "alt_name", :default => "", :null => false
+  end
+
+  create_table "amino_acids", :primary_key => "record_id", :force => true do |t|
+    t.string  "one_letter",                :default => "", :null => false
+    t.string  "three_letter"
+    t.string  "full_name"
+    t.integer "num_H",        :limit => 6, :default => 0
+    t.integer "num_C",        :limit => 6, :default => 0
+    t.integer "num_N",        :limit => 6, :default => 0
+    t.integer "num_O",        :limit => 6, :default => 0
+    t.integer "num_S",        :limit => 6, :default => 0
+  end
+
+  create_table "brick2element", :primary_key => "record_id", :force => true do |t|
+    t.integer "brick_key",                :default => 0,  :null => false
+    t.string  "element",                  :default => "", :null => false
+    t.integer "num_element", :limit => 6, :default => 1
+  end
+
+  create_table "bricks", :primary_key => "record_id", :force => true do |t|
+    t.string "brick",     :default => "", :null => false
+    t.string "full_name"
+  end
+
+  create_table "classifications", :primary_key => "record_id", :force => true do |t|
+    t.string "classification", :default => "", :null => false
+  end
+
+  create_table "elements", :primary_key => "record_id", :force => true do |t|
+    t.string  "element",                                  :default => "",  :null => false
+    t.string  "full_name"
+    t.decimal "mono_mass", :precision => 12, :scale => 9, :default => 0.0, :null => false
+    t.decimal "avge_mass", :precision => 12, :scale => 9, :default => 0.0, :null => false
+  end
+
+  create_table "fragment_comp", :primary_key => "record_id", :force => true do |t|
+    t.integer "fragments_key",              :default => 0,  :null => false
+    t.string  "brick",                      :default => "", :null => false
+    t.integer "num_brick",     :limit => 6, :default => 1
+  end
+
+  create_table "fragments", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key", :default => 0, :null => false
+  end
+
+  create_table "log", :primary_key => "record_id", :force => true do |t|
+    t.datetime "timestamp", :null => false
+    t.text     "query"
+  end
+
+  create_table "mod2brick", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",                :default => 0,  :null => false
+    t.string  "brick",                  :default => "", :null => false
+    t.integer "num_brick", :limit => 6, :default => 1
+  end
+
+  create_table "modifications", :primary_key => "record_id", :force => true do |t|
+    t.string   "full_name",                                                      :default => "", :null => false
+    t.string   "code_name",                                                      :default => "", :null => false
+    t.decimal  "mono_mass",                       :precision => 12, :scale => 6
+    t.decimal  "avge_mass",                       :precision => 12, :scale => 4
+    t.string   "composition"
+    t.text     "misc_notes"
+    t.string   "username_of_poster",                                             :default => "", :null => false
+    t.string   "group_of_poster",                                                :default => "", :null => false
+    t.datetime "date_time_posted",                                                               :null => false
+    t.datetime "date_time_modified",                                                             :null => false
+    t.string   "ex_code_name"
+    t.integer  "approved",           :limit => 4,                                :default => 0
+  end
+
+  create_table "neutral_losses", :primary_key => "record_id", :force => true do |t|
+    t.integer "spec_key",               :default => 0,  :null => false
+    t.string  "brick",                  :default => "", :null => false
+    t.integer "num_brick", :limit => 6, :default => 1
+  end
+
+  create_table "plugin_schema_info", :id => false, :force => true do |t|
+    t.string  "plugin_name"
+    t.integer "version"
+  end
+
+  create_table "positions", :primary_key => "record_id", :force => true do |t|
+    t.string "position", :default => "", :null => false
+  end
+
+  create_table "spec2nl", :primary_key => "record_id", :force => true do |t|
+    t.integer "spec_key",                                                   :default => 0, :null => false
+    t.integer "is_pep_nl",      :limit => 4,                                :default => 0
+    t.integer "is_req_pep_nl",  :limit => 4,                                :default => 0
+    t.integer "is_slave_nl",    :limit => 4,                                :default => 0
+    t.decimal "nl_mono_mass",                :precision => 12, :scale => 6
+    t.decimal "nl_avge_mass",                :precision => 12, :scale => 4
+    t.string  "nl_composition"
+  end
+
+  create_table "specificity", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",                          :default => 0,  :null => false
+    t.string  "one_letter",                       :default => "", :null => false
+    t.integer "position_key",                     :default => 0,  :null => false
+    t.integer "hidden",              :limit => 4, :default => 0
+    t.integer "spec_group",          :limit => 6, :default => 0
+    t.integer "classifications_key",              :default => 0,  :null => false
+    t.text    "misc_notes"
+  end
+
+  create_table "users", :primary_key => "record_id", :force => true do |t|
+    t.string "UserName", :limit => 64
+    t.string "Password", :limit => 64
+    t.string "GroupID",  :limit => 64
+    t.string "FullName"
+    t.string "Email"
+  end
+
+  create_table "xref_sources", :primary_key => "record_id", :force => true do |t|
+    t.string "xref_source", :default => "", :null => false
+  end
+
+  create_table "xrefs", :primary_key => "record_id", :force => true do |t|
+    t.integer "mod_key",         :default => 0, :null => false
+    t.integer "xref_source_key", :default => 0, :null => false
+    t.text    "xref_text"
+    t.string  "xref_url"
+  end
+
+end

data/lib/active_unimod.rb

@@ -0,0 +1,4 @@
+require 'active_record'
+Dir.glob(File.dirname(__FILE__) + "/../app/models/*").each do |model|
+  require model
+end

data/lib/active_unimod/database.rb

@@ -0,0 +1,84 @@
+require 'active_unimod'
+require 'hpricot'
+require 'open-uri'
+require 'logger'
+
+ActiveRecord::Base.logger ||= Logger.new('unimod_log.txt')
+
+module ActiveUnimod
+  
+  # Methods for managing a local Unimod database.  Information
+  # normally logged by Rails will be written to 'unimod_log.txt' 
+  # unless ActiveRecord::Base.logger is set when this file is 
+  # required.
+  #
+  module Database
+    TABLES = [
+    AltName,  AminoAcid, Brick2element, Brick, Classification, 
+    Element, FragmentComp, Fragment, Log,  Mod2brick, Modification, 
+    NeutralLoss, Position,  Spec2nl, Specificity, User, XrefSource, Xref]
+    
+    module_function
+    
+    # Creates the ActiveUnimod tables using the default migration (db/migrate/001_active_unimod_schema)
+    def create_tables(verbose=true)
+      ActiveRecord::Migration.verbose = verbose
+      ActiveRecord::Migrator.migrate(File.dirname(__FILE__) + "/../../db/migrate/")
+    end
+    
+    # Parses the xml into ActiveUnimod records.  If overwrite=true the new
+    # records will replace existing records by with the same id.  Otherwise,
+    # non-existant records will be created and the existing records will
+    # be checked.  Any inconsistent records will be collected and returned
+    # as an array of [new_record, existing_record] arrays.
+    #
+    # Progress is logged to logger.
+    #
+    def update_from_xml(xml, overwrite=false, logger=Logger.new($stdout))
+      doc = Hpricot.XML(xml)
+      inconsistencies = []
+
+      TABLES.each do |table|
+        table.transaction do
+          logger.add(Logger::INFO, "updating: #{table.table_name}")
+
+          rows = doc.search("unimod/#{table.table_name}/#{table.table_name}_row")
+          rows.each do |row|
+            attributes = row.attributes
+            id = attributes.delete("record_id")
+            record = table.new(attributes)
+            record.id = id
+          
+            if table.exists?(id)
+              existing_record = table.find(id) 
+              unless record.attributes == existing_record.attributes
+                if overwrite
+                  logger.add(Logger::INFO, "overwritting: #{id}")
+                  existing_record.attributes = row.attributes
+                  existing_record.save
+                else
+                  inconsistencies << [record, existing_record]
+                end
+              end
+            else
+              logger.add(Logger::INFO, "adding: #{id}")
+              record.save
+            end
+          end
+        end
+      end
+      
+      inconsistencies
+    end
+    
+    # Retrieves the unimod_tables.xml from "http://www.unimod.org/xml/unimod_tables.xml"
+    # and uses this datafile in update_from_xml.
+    def update_from_web(url=nil, overwrite=false, logger=Logger.new($stdout))
+      url = "http://www.unimod.org/xml/unimod_tables.xml" if url == nil
+      
+      logger.add(Logger::INFO, "retrieving: #{url}")
+      update_from_xml(open(url), overwrite, logger)
+    end
+
+  end
+end

data/lib/active_unimod_tasks.rb

@@ -0,0 +1,25 @@
+namespace :active_unimod do
+  namespace :database do 
+    
+    # TODO - add a flag for which way to relsove discrepancies.
+    desc "Updates unimod database from website."
+    task :update do
+      require File.expand_path(RAILS_ROOT + "/config/environment")
+      require 'active_unimod/database'
+      
+      inconsistencies = ActiveUnimod::Database.update_from_web(nil, ENV["OVERWRITE"])
+    
+      unless inconsistencies.empty?
+        require 'pp'
+        puts "found #{inconsistencies.length} inconsistent #{inconsistencies.length > 1 ? 'entries' : 'entry'}:"
+        inconsistencies.each do |record, existing|
+          puts "#{record.class.table_name}(#{record.id})\n  expected #{PP.singleline_pp(record.attributes, "")}\n  but was  #{PP.singleline_pp(existing.attributes, "")}"
+        end
+      
+        puts
+        puts "inconsistent entries WERE NOT updated"
+      end
+    end
+    
+  end  
+end

data/lib/generators/active_unimod/USAGE

@@ -0,0 +1,27 @@
+NAME
+     active_unimod - allows incorporation/usage of a Unimod database
+
+SYNOPSIS
+     active_unimod [path/to/rails_root (default Dir.pwd)]
+     
+DESCRIPTION
+     Creates models and database migrations to setup and utilize a
+     local Unimod database.
+
+     Included:
+      - Models for all the Unimod tables.
+      - A migration to setup these tables.
+      - Tests files and fixtures for each table.
+      - Tasks for working with the local Unimod database.
+      - Use options '--skip-migration' or '--skip-fixtures' to skip 
+        installation of these components.
+        
+EXAMPLE
+      ./script/generate active_unimod 
+
+     This will generate a the models in app/models, install unit test files,
+     fixtures, and a migration in db/migrate.  
+     
+     ./script/generate active_unimod --help
+     
+     Print this help

data/lib/generators/active_unimod/active_unimod_generator.rb

@@ -0,0 +1,82 @@
+class ActiveUnimodGenerator < Rails::Generator::Base # :nodoc:
+  default_options :skip_migration => false, :skip_fixtures => false
+  
+  def initialize(runtime_args, runtime_options = {})
+    super
+    @destination_root = runtime_args.shift || Dir.pwd
+  end
+  
+  def manifest
+    record do |m|
+      m.directory "app/models"
+      m.directory "db/migrate"
+      m.directory "lib/tasks"
+      m.directory "test/fixtures"
+      m.directory "test/unit"
+      
+      m.file "/../../../../lib/active_unimod_tasks.rb",  "lib/tasks/active_unimod_tasks.rake"
+      
+      root = File.expand_path( File.dirname(__FILE__) + "/../../../" )
+      Dir.glob(File.join(root, "app/models/*.rb")).each do |model_file|
+        model = File.basename(model_file).chomp(".rb")
+
+        m.file "/../../../../app/models/#{model}.rb",  File.join('app/models', "#{model}.rb")
+        m.template 'unit_test.rb',  File.join('test/unit', "#{model}_test.rb"), :assigns => {:class_name => model.camelize}
+        unless options[:skip_fixtures] 
+       	  m.template 'fixtures.yml',  File.join('test/fixtures', "#{model}.yml")
+        end
+      end
+      
+      unless options[:skip_migration]
+        @migration_directory = File.join(@destination_root, 'db/migrate')
+        migration_file_name = "active_unimod_schema"
+        if migration_exists?(migration_file_name)
+          raise "Another migration is already named #{migration_file_name}: #{existing_migrations(migration_file_name).first}"
+        end
+        
+        m.file('/../../../../db/migrate/001_active_unimod_schema.rb', "db/migrate/#{next_migration_string}_#{migration_file_name}.rb")
+      end
+    end
+  end
+  
+  protected
+
+  def add_options!(opt)
+    opt.separator ''
+    opt.separator 'Options:'
+    opt.on("--skip-migration", 
+           "Don't generate a migration file for these models") { |v| options[:skip_migration] = v }
+    opt.on("--skip-fixtures",
+           "Don't generation a fixture file for these models") { |v| options[:skip_fixtures] = v}
+  end
+
+  #
+  # The migration_template method makes the migration
+  # file in the wrong place, and the workaround above requires
+  # these protected methods from  'rails-2.0.1\lib\commands.rb'
+  #
+          def existing_migrations(file_name)
+            Dir.glob("#{@migration_directory}/[0-9]*_*.rb").grep(/[0-9]+_#{file_name}.rb$/)
+          end
+
+          def migration_exists?(file_name)
+            not existing_migrations(file_name).empty?
+          end
+
+          def current_migration_number
+            Dir.glob("#{@destination_root}/#{@migration_directory}/[0-9]*_*.rb").inject(0) do |max, file_path|
+              n = File.basename(file_path).split('_', 2).first.to_i
+              if n > max then n else max end
+            end
+          end
+
+          def next_migration_number
+            current_migration_number + 1
+          end
+          
+          def next_migration_string(padding = 3)
+            "%.#{padding}d" % next_migration_number
+          end
+          
+
+end

data/lib/generators/active_unimod/templates/fixtures.yml

@@ -0,0 +1,7 @@
+# Read about fixtures at http://ar.rubyonrails.org/classes/Fixtures.html
+
+# one:
+#   column: value
+#
+# two:
+#   column: value

data/lib/generators/active_unimod/templates/unit_test.rb

@@ -0,0 +1,8 @@
+require File.dirname(__FILE__) + '/../test_helper'
+
+class <%= class_name %>Test < ActiveSupport::TestCase
+  # Replace this with your real tests.
+  def test_truth
+    assert true
+  end
+end

metadata

@@ -0,0 +1,111 @@
+--- !ruby/object:Gem::Specification 
+name: active_unimod_generator
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Simon Chiang
+autorequire: active_unimod
+bindir: bin
+cert_chain: []
+
+date: 2007-12-20 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: activerecord
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.0.1
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: hpricot
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.6.0
+    version: 
+description: 
+email: simon.chiang@uchsc.edu
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README
+- MIT-LICENSE
+- History
+files: 
+- app/models/alt_name.rb
+- app/models/amino_acid.rb
+- app/models/brick.rb
+- app/models/brick2element.rb
+- app/models/classification.rb
+- app/models/element.rb
+- app/models/fragment.rb
+- app/models/fragment_comp.rb
+- app/models/log.rb
+- app/models/mod2brick.rb
+- app/models/modification.rb
+- app/models/neutral_loss.rb
+- app/models/position.rb
+- app/models/spec2nl.rb
+- app/models/specificity.rb
+- app/models/user.rb
+- app/models/xref.rb
+- app/models/xref_source.rb
+- db/migrate
+- db/migrate/001_active_unimod_schema.rb
+- db/schema.rb
+- lib/active_unimod
+- lib/active_unimod/database.rb
+- lib/active_unimod.rb
+- lib/active_unimod_tasks.rb
+- lib/generators
+- lib/generators/active_unimod
+- lib/generators/active_unimod/active_unimod_generator.rb
+- lib/generators/active_unimod/templates
+- lib/generators/active_unimod/templates/fixtures.yml
+- lib/generators/active_unimod/templates/unit_test.rb
+- lib/generators/active_unimod/USAGE
+- Rakefile
+- active_unimod_generator.rb
+- README
+- MIT-LICENSE
+- History
+has_rdoc: true
+homepage: http://rubyforge.org/projects/bioactive/active_unimod
+post_install_message: 
+rdoc_options: 
+- --title
+- ActiveUnimod
+- --main
+- README
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 0.9.5
+signing_key: 
+specification_version: 2
+summary: ActiveRecord models and database migrations for Unimod.
+test_files: []
+