bio-sra 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 48531f3fc7b4facb8b4ed2b4523f6ab5eabb6897
+  data.tar.gz: 1ce0ebaccc4601144aa0150caf2913e2c3d96de1
+SHA512:
+  metadata.gz: 3a81f703d495b138cb4a2d53ec2cced77fe888cd6f505ca28c9bec2bb20cddff4ca3b57c2b7cfcf31f8eda5fe00679d1bab503c91423f1f66ab141028ddf10c0
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data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'activerecord', '~> 3.2'
+gem "activesupport", "~> 3.2"
+gem "sqlite3", "~> 1.3"
+gem 'bio-logger', '~> 1.0'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", "~> 3.5"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 2.0", '>= 2.0.1'
+  gem "bundler", "~> 1.6"
+  gem "bio", '~>1.4', ">= 1.4.2"
+
+  gem 'bio-commandeer', '~>0.1'
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J. Woodcroft
+
+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.md

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+# bio-sra
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-sra.png)](http://travis-ci.org/wwood/bioruby-sra)
+
+A Sequence Read Archive (SRA) download script and Ruby interface to the [SRAdb](ncbi.nlm.nih.gov/pmc/articles/PMC3560148/) (SRA metadata) SQLite database.
+
+## Installation
+
+```sh
+gem install bio-sra
+```
+
+## Download script usage
+
+Download a single run file to the current directory:
+```sh
+sra_download --runs ERR229501.sra
+```
+
+Download a list of runs
+```sh
+$ cat srr_list.txt
+ERR229501
+ERR229498
+$ sra_download --runs -f srr_list.txt
+```
+
+Download all runs that are a part of the experiment ERP001779 (Microbial biogeography of public restroom surfaces)
+```sh
+$ sra_download ERP001779
+```
+This finds ERP001779 and links it to runs through the SRAdb
+
+## Ruby interface script
+
+```ruby
+require 'bio-sra'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/bioruby-sra
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+This Ruby code is unpublished, but there's a problem with
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-sra](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-sra"
+  gem.homepage = "http://github.com/wwood/bioruby-sra"
+  gem.license = "MIT"
+  gem.summary = %Q{A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database}
+  gem.description = %Q{A Sequence Read Archive (SRA) download script and Ruby interface to the SRAdb (SRA metadata) SQLite database.}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-sra #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end# encoding: utf-8
+Encoding.default_external = Encoding::UTF_8
+
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__),'lib')
+require 'active_support'
+require 'active_support/core_ext/class/attribute_accessors'
+require 'active_support/core_ext/module/delegation'
+require 'active_record'
+
+namespace :db do
+  namespace :schema do
+    desc 'Dump out the schema in markdown format suitable for inclusion at https://github.com/wwood/bioruby-sra/wiki/MetadatabaseSchema'
+    task :dump_wiki_format do
+      require 'bio-sra'
+      include Bio::SRA::Tables
+      Bio::SRA.connect
+
+      # grep 'class ' lib/bio/sra/tables.rb |awk '{print $2}'
+      tables = [
+        Submission,
+        Experiment,
+        Study,
+        Sample,
+        Run,
+        SRA,
+        SRAFt,
+        SRAFtContent,
+        SRAFtSegDir,
+        SRAFtSegments,
+        MetaInfo,
+        ColDesc]
+      tables.each do |table|
+        puts "### The table '#{table.table_name}'"
+        puts "bioruby-sra class name: #{table.to_s.gsub('Bio::SRA::Tables::','')}"
+        puts
+        documented_columns = ColDesc.where(:table_name => table.table_name).order('field_name').all.collect do |c|
+          f = c.field_name
+          unless table.first.respond_to?(f.to_sym) #e.g. ID => submission_ID
+            f = "#{c.table_name}_#{f}"
+          end
+          if table.first.respond_to?(f.to_sym)
+            examples = table.limit(2).where("#{f} not null").select("distinct(#{f})").all.collect{|e| e.send(f.to_sym)}
+            examples.collect! do |eg|
+              if eg.kind_of?(String) and eg.length > 50
+                eg[0..49]+'..'
+              else
+                eg
+              end
+            end
+            examples.collect!{|eg| eg.to_s.gsub('_','\_').strip}
+            print "* **#{f}** #{c.description.gsub('_','\_')} "+
+              "(#{c.type}) "
+            if examples[0].to_s.length > 0
+              puts "e.g. _#{examples.join('_, _')}_"
+            else
+              puts '_(currently always null in the database)_'
+            end
+            f
+          else
+            nil
+          end
+        end
+        undocumented_columns = table.content_columns.collect{|col| col.name}.reject{|col| documented_columns.include?(col)}
+        if !undocumented_columns.empty?
+          puts
+          puts 'Currently undocumented columns: '+undocumented_columns.sort.join(', ')
+        end
+        puts
+        puts
+      end
+    end
+  end
+end
+
+#This code is coming from activerecord-3.0.7/lib/active_record/railties/databases.rake
+namespace :db do
+  task :load_config do
+    require 'active_record'
+    ActiveRecord::Base.configurations = YAML.load_file("config/database.yml")
+  end
+
+  task :environment => :load_config do
+    ActiveRecord::Base.establish_connection('default')
+  end
+
+  namespace :create do
+    # desc 'Create all the local databases defined in config/database.yml'
+    task :all => :load_config do
+      ActiveRecord::Base.configurations.each_value do |config|
+        # Skip entries that don't have a database key, such as the first entry here:
+        #
+        #  defaults: &defaults
+        #    adapter: mysql
+        #    username: root
+        #    password:
+        #    host: localhost
+        #
+        #  development:
+        #    database: blog_development
+        #    <<: *defaults
+        next unless config['database']
+        # Only connect to local databases
+        local_database?(config) { create_database(config) }
+      end
+    end
+  end
+
+  desc 'Create the database from config/database.yml for the current default (use db:create:all to create all dbs in the config)'
+  task :create => :load_config do
+    # Make the test database at the same time as the development one, if it exists
+#    if 'default'.development? && ActiveRecord::Base.configurations['test']
+      create_database(ActiveRecord::Base.configurations['default'])
+#    end
+#    create_database(ActiveRecord::Base.configurations['default'])
+  end
+
+  def create_database(config)
+    begin
+      if config['adapter'] =~ /sqlite/
+        if File.exist?(config['database'])
+          $stderr.puts "#{config['database']} already exists"
+        else
+          begin
+            # Create the SQLite database
+            ActiveRecord::Base.establish_connection(config)
+            ActiveRecord::Base.connection
+          rescue Exception => e
+            $stderr.puts e, *(e.backtrace)
+            $stderr.puts "Couldn't create database for #{config.inspect}"
+          end
+        end
+        return # Skip the else clause of begin/rescue
+      else
+        ActiveRecord::Base.establish_connection(config)
+        ActiveRecord::Base.connection
+      end
+    rescue
+      case config['adapter']
+      when /mysql/
+        @charset   = ENV['CHARSET']   || 'utf8'
+        @collation = ENV['COLLATION'] || 'utf8_unicode_ci'
+        creation_options = {:charset => (config['charset'] || @charset), :collation => (config['collation'] || @collation)}
+        error_class = config['adapter'] =~ /mysql2/ ? Mysql2::Error : Mysql::Error
+        access_denied_error = 1045
+        begin
+          ActiveRecord::Base.establish_connection(config.merge('database' => nil))
+          ActiveRecord::Base.connection.create_database(config['database'], creation_options)
+          ActiveRecord::Base.establish_connection(config)
+        rescue error_class => sqlerr
+          if sqlerr.errno == access_denied_error
+            print "#{sqlerr.error}. \nPlease provide the root password for your mysql installation\n>"
+            root_password = $stdin.gets.strip
+            grant_statement = "GRANT ALL PRIVILEGES ON #{config['database']}.* " \
+              "TO '#{config['username']}'@'localhost' " \
+              "IDENTIFIED BY '#{config['password']}' WITH GRANT OPTION;"
+            ActiveRecord::Base.establish_connection(config.merge(
+                'database' => nil, 'username' => 'root', 'password' => root_password))
+            ActiveRecord::Base.connection.create_database(config['database'], creation_options)
+            ActiveRecord::Base.connection.execute grant_statement
+            ActiveRecord::Base.establish_connection(config)
+          else
+            $stderr.puts sqlerr.error
+            $stderr.puts "Couldn't create database for #{config.inspect}, charset: #{config['charset'] || @charset}, collation: #{config['collation'] || @collation}"
+            $stderr.puts "(if you set the charset manually, make sure you have a matching collation)" if config['charset']
+          end
+        end
+      when 'postgresql'
+        @encoding = config['encoding'] || ENV['CHARSET'] || 'utf8'
+        begin
+          ActiveRecord::Base.establish_connection(config.merge('database' => 'postgres', 'schema_search_path' => 'public'))
+          ActiveRecord::Base.connection.create_database(config['database'], config.merge('encoding' => @encoding))
+          ActiveRecord::Base.establish_connection(config)
+        rescue Exception => e
+          $stderr.puts e, *(e.backtrace)
+          $stderr.puts "Couldn't create database for #{config.inspect}"
+        end
+      end
+    else
+      $stderr.puts "#{config['database']} already exists"
+    end
+  end
+
+  namespace :drop do
+    # desc 'Drops all the local databases defined in config/database.yml'
+    task :all => :load_config do
+      ActiveRecord::Base.configurations.each_value do |config|
+        # Skip entries that don't have a database key
+        next unless config['database']
+        begin
+          # Only connect to local databases
+          local_database?(config) { drop_database(config) }
+        rescue Exception => e
+          $stderr.puts "Couldn't drop #{config['database']} : #{e.inspect}"
+        end
+      end
+    end
+  end
+
+  desc 'Drops the database for the current default (use db:drop:all to drop all databases)'
+  task :drop => :load_config do
+    config = ActiveRecord::Base.configurations['default' || 'development']
+    begin
+      drop_database(config)
+    rescue Exception => e
+      $stderr.puts "Couldn't drop #{config['database']} : #{e.inspect}"
+    end
+  end
+
+  def local_database?(config, &block)
+    if %w( 127.0.0.1 localhost ).include?(config['host']) || config['host'].blank?
+      yield
+    else
+      $stderr.puts "This task only modifies local databases. #{config['database']} is on a remote host."
+    end
+  end
+
+  desc "Migrate the database (options: VERSION=x, VERBOSE=false)."
+  task :migrate => :environment do
+    ActiveRecord::Migration.verbose = ENV["VERBOSE"] ? ENV["VERBOSE"] == "true" : true
+    ActiveRecord::Migrator.migrate("db/migrate/", ENV["VERSION"] ? ENV["VERSION"].to_i : nil)
+    Rake::Task["db:schema:dump"].invoke if ActiveRecord::Base.schema_format == :ruby
+  end
+
+  namespace :migrate do
+    # desc  'Rollbacks the database one migration and re migrate up (options: STEP=x, VERSION=x).'
+    task :redo => :environment do
+      if ENV["VERSION"]
+        Rake::Task["db:migrate:down"].invoke
+        Rake::Task["db:migrate:up"].invoke
+      else
+        Rake::Task["db:rollback"].invoke
+        Rake::Task["db:migrate"].invoke
+      end
+    end
+
+    # desc 'Resets your database using your migrations for the current environment'
+    task :reset => ["db:drop", "db:create", "db:migrate"]
+
+    # desc 'Runs the "up" for a given migration VERSION.'
+    task :up => :environment do
+      version = ENV["VERSION"] ? ENV["VERSION"].to_i : nil
+      raise "VERSION is required" unless version
+      ActiveRecord::Migrator.run(:up, "db/migrate/", version)
+      Rake::Task["db:schema:dump"].invoke if ActiveRecord::Base.schema_format == :ruby
+    end
+
+    # desc 'Runs the "down" for a given migration VERSION.'
+    task :down => :environment do
+      version = ENV["VERSION"] ? ENV["VERSION"].to_i : nil
+      raise "VERSION is required" unless version
+      ActiveRecord::Migrator.run(:down, "db/migrate/", version)
+      Rake::Task["db:schema:dump"].invoke if ActiveRecord::Base.schema_format == :ruby
+    end
+
+    desc "Display status of migrations"
+    task :status => :environment do
+      config = ActiveRecord::Base.configurations['default']
+      ActiveRecord::Base.establish_connection(config)
+      unless ActiveRecord::Base.connection.table_exists?(ActiveRecord::Migrator.schema_migrations_table_name)
+        puts 'Schema migrations table does not exist yet.'
+        next  # means "return" for rake task
+      end
+      db_list = ActiveRecord::Base.connection.select_values("SELECT version FROM #{ActiveRecord::Migrator.schema_migrations_table_name}")
+      file_list = []
+      Dir.foreach(File.join('db', 'migrate')) do |file|
+        # only files matching "20091231235959_some_name.rb" pattern
+        if match_data = /(\d{14})_(.+)\.rb/.match(file)
+          status = db_list.delete(match_data[1]) ? 'up' : 'down'
+          file_list << [status, match_data[1], match_data[2]]
+        end
+      end
+      # output
+      puts "\ndatabase: #{config['database']}\n\n"
+      puts "#{"Status".center(8)}  #{"Migration ID".ljust(14)}  Migration Name"
+      puts "-" * 50
+      file_list.each do |file|
+        puts "#{file[0].center(8)}  #{file[1].ljust(14)}  #{file[2].humanize}"
+      end
+      db_list.each do |version|
+        puts "#{'up'.center(8)}  #{version.ljust(14)}  *** NO FILE ***"
+      end
+      puts
+    end
+  end
+
+  desc 'Rolls the schema back to the previous version (specify steps w/ STEP=n).'
+  task :rollback => :environment do
+    step = ENV['STEP'] ? ENV['STEP'].to_i : 1
+    ActiveRecord::Migrator.rollback('db/migrate/', step)
+    Rake::Task["db:schema:dump"].invoke if ActiveRecord::Base.schema_format == :ruby
+  end
+
+  # desc 'Pushes the schema to the next version (specify steps w/ STEP=n).'
+  task :forward => :environment do
+    step = ENV['STEP'] ? ENV['STEP'].to_i : 1
+    ActiveRecord::Migrator.forward('db/migrate/', step)
+    Rake::Task["db:schema:dump"].invoke if ActiveRecord::Base.schema_format == :ruby
+  end
+
+  # desc 'Drops and recreates the database from db/schema.rb for the current environment and loads the seeds.'
+  task :reset => [ 'db:drop', 'db:setup' ]
+
+  # desc "Retrieves the charset for the current environment's database"
+  task :charset => :environment do
+    config = ActiveRecord::Base.configurations['default' || 'development']
+    case config['adapter']
+    when /mysql/
+      ActiveRecord::Base.establish_connection(config)
+      puts ActiveRecord::Base.connection.charset
+    when 'postgresql'
+      ActiveRecord::Base.establish_connection(config)
+      puts ActiveRecord::Base.connection.encoding
+    when 'sqlite3'
+      ActiveRecord::Base.establish_connection(config)
+      puts ActiveRecord::Base.connection.encoding
+    else
+      $stderr.puts 'sorry, your database adapter is not supported yet, feel free to submit a patch'
+    end
+  end
+
+  # desc "Retrieves the collation for the current environment's database"
+  task :collation => :environment do
+    config = ActiveRecord::Base.configurations['default']
+    case config['adapter']
+    when /mysql/
+      ActiveRecord::Base.establish_connection(config)
+      puts ActiveRecord::Base.connection.collation
+    else
+      $stderr.puts 'sorry, your database adapter is not supported yet, feel free to submit a patch'
+    end
+  end
+
+  desc "Retrieves the current schema version number"
+  task :version => :environment do
+    puts "Current version: #{ActiveRecord::Migrator.current_version}"
+  end
+
+  # desc "Raises an error if there are pending migrations"
+  task :abort_if_pending_migrations => :environment do
+    if defined? ActiveRecord
+      pending_migrations = ActiveRecord::Migrator.new(:up, 'db/migrate').pending_migrations
+
+      if pending_migrations.any?
+        puts "You have #{pending_migrations.size} pending migrations:"
+        pending_migrations.each do |pending_migration|
+          puts '  %4d %s' % [pending_migration.version, pending_migration.name]
+        end
+        abort %{Run "rake db:migrate" to update your database then try again.}
+      end
+    end
+  end
+
+  desc 'Create the database, load the schema, and initialize with the seed data (use db:reset to also drop the db first)'
+  task :setup => [ 'db:create', 'db:schema:load', 'db:seed' ]
+
+  desc 'Load the seed data from db/seeds.rb'
+  task :seed => 'db:abort_if_pending_migrations' do
+    seed_file = File.join('db', 'seeds.rb')
+    load(seed_file) if File.exist?(seed_file)
+  end
+
+  namespace :fixtures do
+    desc "Load fixtures into the current environment's database.  Load specific fixtures using FIXTURES=x,y. Load from subdirectory in test/fixtures using FIXTURES_DIR=z. Specify an alternative path (eg. spec/fixtures) using FIXTURES_PATH=spec/fixtures."
+    task :load => :environment do
+      require 'active_record/fixtures'
+
+      ActiveRecord::Base.establish_connection('default')
+      base_dir = ENV['FIXTURES_PATH'] ? File.join(ENV['FIXTURES_PATH']) : File.join('test', 'fixtures')
+      fixtures_dir = ENV['FIXTURES_DIR'] ? File.join(base_dir, ENV['FIXTURES_DIR']) : base_dir
+
+      (ENV['FIXTURES'] ? ENV['FIXTURES'].split(/,/).map {|f| File.join(fixtures_dir, f) } : Dir["#{fixtures_dir}/**/*.{yml,csv}"]).each do |fixture_file|
+        ActiveRecord::Fixtures.create_fixtures(fixtures_dir, fixture_file[(fixtures_dir.size + 1)..-5])
+      end
+    end
+
+    # desc "Search for a fixture given a LABEL or ID. Specify an alternative path (eg. spec/fixtures) using FIXTURES_PATH=spec/fixtures."
+    task :identify => :environment do
+      require 'active_record/fixtures'
+
+      label, id = ENV["LABEL"], ENV["ID"]
+      raise "LABEL or ID required" if label.blank? && id.blank?
+
+      puts %Q(The fixture ID for "#{label}" is #{Fixtures.identify(label)}.) if label
+
+      base_dir = ENV['FIXTURES_PATH'] ? File.join(ENV['FIXTURES_PATH']) : File.join('test', 'fixtures')
+      Dir["#{base_dir}/**/*.yml"].each do |file|
+        if data = YAML::load(ERB.new(IO.read(file)).result)
+          data.keys.each do |key|
+            key_id = Fixtures.identify(key)
+
+            if key == label || key_id == id.to_i
+              puts "#{file}: #{key} (#{key_id})"
+            end
+          end
+        end
+      end
+    end
+  end
+
+  namespace :schema do
+    desc "Create a db/schema.rb file that can be portably used against any DB supported by AR"
+    task :dump => :environment do
+      require 'active_record/schema_dumper'
+      File.open(ENV['SCHEMA'] || "db/schema.rb", "w") do |file|
+        ActiveRecord::SchemaDumper.dump(ActiveRecord::Base.connection, file)
+      end
+      Rake::Task["db:schema:dump"].reenable
+    end
+
+    desc "Load a schema.rb file into the database"
+    task :load => :environment do
+      file = ENV['SCHEMA'] || "db/schema.rb"
+      if File.exists?(file)
+        load(file)
+      else
+        abort %{#{file} doesn't exist yet. Run "rake db:migrate" to create it then try again. If you do not intend to use a database, you should instead alter config/application.rb to limit the frameworks that will be loaded}
+      end
+    end
+  end
+
+  namespace :structure do
+    desc "Dump the database structure to an SQL file"
+    task :dump => :environment do
+      abcs = ActiveRecord::Base.configurations
+      case abcs['default']["adapter"]
+      when /mysql/, "oci", "oracle"
+        ActiveRecord::Base.establish_connection(abcs['default'])
+        File.open("db/#{'default'}_structure.sql", "w+") { |f| f << ActiveRecord::Base.connection.structure_dump }
+      when "postgresql"
+        ENV['PGHOST']     = abcs['default']["host"] if abcs['default']["host"]
+        ENV['PGPORT']     = abcs['default']["port"].to_s if abcs['default']["port"]
+        ENV['PGPASSWORD'] = abcs['default']["password"].to_s if abcs['default']["password"]
+        search_path = abcs['default']["schema_search_path"]
+        unless search_path.blank?
+          search_path = search_path.split(",").map{|search_path| "--schema=#{search_path.strip}" }.join(" ")
+        end
+        `pg_dump -i -U "#{abcs['default']["username"]}" -s -x -O -f db/default_structure.sql #{search_path} #{abcs['default']["database"]}`
+        raise "Error dumping database" if $?.exitstatus == 1
+      when "sqlite", "sqlite3"
+        dbfile = abcs['default']["database"] || abcs['default']["dbfile"]
+        `#{abcs['default']["adapter"]} #{dbfile} .schema > db/#{'default'}_structure.sql`
+      when "sqlserver"
+        `scptxfr /s #{abcs['default']["host"]} /d #{abcs['default']["database"]} /I /f db\\#{'default'}_structure.sql /q /A /r`
+        `scptxfr /s #{abcs['default']["host"]} /d #{abcs['default']["database"]} /I /F db\ /q /A /r`
+      when "firebird"
+        set_firebird_env(abcs['default'])
+        db_string = firebird_db_string(abcs['default'])
+        sh "isql -a #{db_string} > db/#{'default'}_structure.sql"
+      else
+        raise "Task not supported by '#{abcs['default']["adapter"]}'"
+      end
+
+      if ActiveRecord::Base.connection.supports_migrations?
+        File.open("db/#{'default'}_structure.sql", "a") { |f| f << ActiveRecord::Base.connection.dump_schema_information }
+      end
+    end
+  end
+
+  namespace :test do
+    # desc "Recreate the test database from the current schema.rb"
+    task :load => 'db:test:purge' do
+      ActiveRecord::Base.establish_connection(ActiveRecord::Base.configurations['test'])
+      ActiveRecord::Schema.verbose = false
+      Rake::Task["db:schema:load"].invoke
+    end
+
+    # desc "Recreate the test database from the current environment's database schema"
+    task :clone => %w(db:schema:dump db:test:load)
+
+    # desc "Recreate the test databases from the development structure"
+    task :clone_structure => [ "db:structure:dump", "db:test:purge" ] do
+      abcs = ActiveRecord::Base.configurations
+      case abcs["test"]["adapter"]
+      when /mysql/
+        ActiveRecord::Base.establish_connection(:test)
+        ActiveRecord::Base.connection.execute('SET foreign_key_checks = 0')
+        IO.readlines("db/#{'default'}_structure.sql").join.split("\n\n").each do |table|
+          ActiveRecord::Base.connection.execute(table)
+        end
+      when "postgresql"
+        ENV['PGHOST']     = abcs["test"]["host"] if abcs["test"]["host"]
+        ENV['PGPORT']     = abcs["test"]["port"].to_s if abcs["test"]["port"]
+        ENV['PGPASSWORD'] = abcs["test"]["password"].to_s if abcs["test"]["password"]
+        `psql -U "#{abcs["test"]["username"]}" -f db/#{'default'}_structure.sql #{abcs["test"]["database"]}`
+      when "sqlite", "sqlite3"
+        dbfile = abcs["test"]["database"] || abcs["test"]["dbfile"]
+        `#{abcs["test"]["adapter"]} #{dbfile} < db/#{'default'}_structure.sql`
+      when "sqlserver"
+        `osql -E -S #{abcs["test"]["host"]} -d #{abcs["test"]["database"]} -i db\\#{'default'}_structure.sql`
+      when "oci", "oracle"
+        ActiveRecord::Base.establish_connection(:test)
+        IO.readlines("db/#{'default'}_structure.sql").join.split(";\n\n").each do |ddl|
+          ActiveRecord::Base.connection.execute(ddl)
+        end
+      when "firebird"
+        set_firebird_env(abcs["test"])
+        db_string = firebird_db_string(abcs["test"])
+        sh "isql -i db/#{'default'}_structure.sql #{db_string}"
+      else
+        raise "Task not supported by '#{abcs["test"]["adapter"]}'"
+      end
+    end
+
+    # desc "Empty the test database"
+    task :purge => :environment do
+      abcs = ActiveRecord::Base.configurations
+      case abcs["test"]["adapter"]
+      when /mysql/
+        ActiveRecord::Base.establish_connection(:test)
+        ActiveRecord::Base.connection.recreate_database(abcs["test"]["database"], abcs["test"])
+      when "postgresql"
+        ActiveRecord::Base.clear_active_connections!
+        drop_database(abcs['test'])
+        create_database(abcs['test'])
+      when "sqlite","sqlite3"
+        dbfile = abcs["test"]["database"] || abcs["test"]["dbfile"]
+        File.delete(dbfile) if File.exist?(dbfile)
+      when "sqlserver"
+        dropfkscript = "#{abcs["test"]["host"]}.#{abcs["test"]["database"]}.DP1".gsub(/\\/,'-')
+        `osql -E -S #{abcs["test"]["host"]} -d #{abcs["test"]["database"]} -i db\\#{dropfkscript}`
+        `osql -E -S #{abcs["test"]["host"]} -d #{abcs["test"]["database"]} -i db\\#{'default'}_structure.sql`
+      when "oci", "oracle"
+        ActiveRecord::Base.establish_connection(:test)
+        ActiveRecord::Base.connection.structure_drop.split(";\n\n").each do |ddl|
+          ActiveRecord::Base.connection.execute(ddl)
+        end
+      when "firebird"
+        ActiveRecord::Base.establish_connection(:test)
+        ActiveRecord::Base.connection.recreate_database!
+      else
+        raise "Task not supported by '#{abcs["test"]["adapter"]}'"
+      end
+    end
+
+    # desc 'Check for pending migrations and load the test schema'
+    task :prepare => 'db:abort_if_pending_migrations' do
+      if defined?(ActiveRecord) && !ActiveRecord::Base.configurations.blank?
+        Rake::Task[{ :sql  => "db:test:clone_structure", :ruby => "db:test:load" }[ActiveRecord::Base.schema_format]].invoke
+      end
+    end
+  end
+
+  namespace :sessions do
+    # desc "Creates a sessions migration for use with ActiveRecord::SessionStore"
+    task :create => :environment do
+      raise "Task unavailable to this database (no migration support)" unless ActiveRecord::Base.connection.supports_migrations?
+      require 'rails/generators'
+      Rails::Generators.configure!
+      require 'rails/generators/rails/session_migration/session_migration_generator'
+      Rails::Generators::SessionMigrationGenerator.start [ ENV["MIGRATION"] || "add_sessions_table" ]
+    end
+
+    # desc "Clear the sessions table"
+    task :clear => :environment do
+      ActiveRecord::Base.connection.execute "DELETE FROM #{session_table_name}"
+    end
+  end
+end
+
+task 'test:prepare' => 'db:test:prepare'
+
+def drop_database(config)
+  case config['adapter']
+  when /mysql/
+    ActiveRecord::Base.establish_connection(config)
+    ActiveRecord::Base.connection.drop_database config['database']
+  when /^sqlite/
+    require 'pathname'
+    path = Pathname.new(config['database'])
+    file = path.absolute? ? path.to_s : File.join( path)
+
+    FileUtils.rm(file)
+  when 'postgresql'
+    ActiveRecord::Base.establish_connection(config.merge('database' => 'postgres', 'schema_search_path' => 'public'))
+    ActiveRecord::Base.connection.drop_database config['database']
+  end
+end
+
+def session_table_name
+  ActiveRecord::SessionStore::Session.table_name
+end
+
+def set_firebird_env(config)
+  ENV["ISC_USER"]     = config["username"].to_s if config["username"]
+  ENV["ISC_PASSWORD"] = config["password"].to_s if config["password"]
+end
+
+def firebird_db_string(config)
+  FireRuby::Database.db_string_for(config.symbolize_keys)
+end