MARQ 0.0.1

data/merb/autotest/merb_rspec.rb

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+# Adapted from Autotest::Rails, RSpec's autotest class, as well as merb-core's.
+require 'autotest'
+
+class RspecCommandError < StandardError; end
+
+# This class maps your application's structure so Autotest can understand what 
+# specs to run when files change.
+#
+# Fixtures are _not_ covered by this class. If you change a fixture file, you 
+# will have to run your spec suite manually, or, better yet, provide your own 
+# Autotest map explaining how your fixtures are set up.
+class Autotest::MerbRspec < Autotest
+  def initialize
+    super
+
+    # Ignore any happenings in these directories
+    add_exception %r%^\./(?:doc|log|public|tmp|\.git|\.hg|\.svn|framework|gems|schema|\.DS_Store|autotest|bin|.*\.sqlite3)% 
+    # Ignore SCM directories and custom Autotest mappings
+    %w[.svn .hg .git .autotest].each { |exception| add_exception(exception) }
+
+    # Ignore any mappings that Autotest may have already set up
+    clear_mappings
+
+    # Anything in /lib could have a spec anywhere, if at all. So, look for
+    # files with roughly the same name as the file in /lib
+    add_mapping %r%^lib\/(.*)\.rb% do |_, m|
+      files_matching %r%^spec\/#{m[1]}%
+    end
+
+    add_mapping %r%^spec/(spec_helper|shared/.*)\.rb$% do
+      all_specs
+    end
+
+    # Changing a spec will cause it to run itself
+    add_mapping %r%^spec/.*\.rb$% do |filename, _|
+      filename
+    end
+
+    # Any change to a model will cause it's corresponding test to be run
+    add_mapping %r%^app/models/(.*)\.rb$% do |_, m|
+      spec_for(m[1], 'model')
+    end
+
+    # Any change to global_helpers will result in all view and controller
+    # tests being run
+    add_mapping %r%^app/helpers/global_helpers\.rb% do
+      files_matching %r%^spec/(views|controllers|helpers)/.*_spec\.rb$%
+    end
+
+    # Any change to a helper will cause its spec to be run
+    add_mapping %r%^app/helpers/((.*)_helper(s)?)\.rb% do |_, m|
+      spec_for(m[1], 'helper')
+    end
+
+    # Changes to a view cause its spec to be run
+    add_mapping %r%^app/views/(.*)/% do |_, m|
+      spec_for(m[1], 'view')
+    end
+
+    # Changes to a controller result in its corresponding spec being run. If
+    # the controller is the exception or application controller, all
+    # controller specs are run.
+    add_mapping %r%^app/controllers/(.*)\.rb$% do |_, m|
+      if ["application", "exception"].include?(m[1])
+        files_matching %r%^spec/controllers/.*_spec\.rb$%
+      else
+        spec_for(m[1], 'controller')
+      end
+    end
+
+    # If a change is made to the router, run controller, view and helper specs
+    add_mapping %r%^config/router.rb$% do
+      files_matching %r%^spec/(controllers|views|helpers)/.*_spec\.rb$%
+    end
+
+    # If any of the major files governing the environment are altered, run
+    # everything
+    add_mapping %r%^config/(init|rack|environments/test).*\.rb|database\.yml% do 
+      all_specs
+    end
+  end
+
+  def failed_results(results)
+    results.scan(/^\d+\)\n(?:\e\[\d*m)?(?:.*?Error in )?'([^\n]*)'(?: FAILED)?(?:\e\[\d*m)?\n(.*?)\n\n/m)
+  end
+
+  def handle_results(results)
+    @failures      = failed_results(results)
+    @files_to_test = consolidate_failures(@failures)
+    @files_to_test.empty? && !$TESTING ? hook(:green) : hook(:red)
+    @tainted = !@files_to_test.empty?
+  end
+
+  def consolidate_failures(failed)
+    filters = Hash.new { |h,k| h[k] = [] }
+    failed.each do |spec, failed_trace|
+      if f = test_files_for(failed).find { |f| f =~ /spec\// }
+        filters[f] << spec
+        break
+      end
+    end
+    filters
+  end
+
+  def make_test_cmd(specs_to_runs)
+    [
+      ruby,
+      "-S",
+      spec_command,
+      add_options_if_present,
+      files_to_test.keys.flatten.join(' ')
+    ].join(' ')
+  end
+
+  def add_options_if_present
+    File.exist?("spec/spec.opts") ? "-O spec/spec.opts " : ""
+  end
+
+  # Finds the proper spec command to use. Precendence is set in the
+  # lazily-evaluated method spec_commands.  Alias + Override that in
+  # ~/.autotest to provide a different spec command then the default
+  # paths provided.
+  def spec_command(separator=File::ALT_SEPARATOR)
+    unless defined?(@spec_command)
+      @spec_command = spec_commands.find { |cmd| File.exists?(cmd) }
+
+      raise RspecCommandError, "No spec command could be found" unless @spec_command
+
+      @spec_command.gsub!(File::SEPARATOR, separator) if separator
+    end
+    @spec_command
+  end
+
+  # Autotest will look for spec commands in the following
+  # locations, in this order:
+  #
+  #   * default spec bin/loader installed in Rubygems
+  #   * any spec command found in PATH
+  def spec_commands
+    [File.join(Config::CONFIG['bindir'], 'spec'), 'spec']
+  end
+
+private
+
+  # Runs +files_matching+ for all specs
+  def all_specs
+    files_matching %r%^spec/.*_spec\.rb$%
+  end
+
+  # Generates a path to some spec given its kind and the match from a mapping
+  #
+  # ==== Arguments
+  # match<String>:: the match from a mapping
+  # kind<String>:: the kind of spec that the match represents
+  #
+  # ==== Returns
+  # String
+  #
+  # ==== Example
+  #   > spec_for('post', :view')
+  #   => "spec/views/post_spec.rb"
+  def spec_for(match, kind)
+    File.join("spec", kind + 's', "#{match}_spec.rb")
+  end
+end

data/merb/config.ru

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+require 'fileutils'
+
+ENV['GEM_HOME']="/home/marq/.ruby/gems/"
+ENV['GEM_PATH']="/home/marq/.ruby/gems/:/var/lib/gems/1.8/"
+require 'rubygems'
+require 'rubygems'
+
+ENV['RBBT_HOME'] = '/home/marq/git/rbbt/'
+$:.unshift(File.join(ENV['RBBT_HOME'], 'lib'))
+require 'rbbt/bow/dictionary'
+
+ENV['MARQ_HOME'] = '/home/marq/git/MARQ/'
+$:.unshift(File.join(ENV['MARQ_HOME'], 'lib'))
+$:.unshift(File.join(ENV['MARQ_HOME'], 'merb'))
+
+require 'MARQ'
+
+require 'merb-core'
+
+def init_WS
+  if File.exists?('tmp/ws.pid')
+    begin
+      Process.kill(9, File.open('tmp/ws.pid').read.to_i)
+    rescue
+    ensure
+      FileUtils.rm 'tmp/ws.pid'
+    end
+    sleep 2
+  end
+
+  pid = fork do
+      FileUtils.cd File.join(MARQ.rootdir, 'webservice')
+      require 'MARQWS'
+     
+  
+      puts "Starting WS"
+      host = `hostname`.chomp.strip + '.' +  `hostname -d`.chomp.strip
+      port = '8282'
+  
+      puts "Starting Server in #{ host }:#{ port }"
+      server = MARQWS.new("MARQ", "MARQ Web Server",host, port, MARQ.workdir)
+  
+      FileUtils.mkdir_p File.join(MARQ.rootdir, '/webservice/wsdl/') unless File.exist? File.join(MARQ.rootdir, '/webservice/wsdl/')
+      Open.write(File.join(MARQ.rootdir, '/webservice/wsdl/MARQWS.wsdl'), server.wsdl)
+  
+      trap('INT') { server.shutdown }
+      server.start
+  end
+  File.open('tmp/ws.pid','w'){|f| f.puts pid}
+  sleep 2
+end
+
+require 'soap/wsdlDriver'
+begin
+    
+    SOAP::WSDLDriverFactory.new(File.join(MARQ.rootdir, '/webservice/wsdl/MARQWS.wsdl')).create_rpc_driver.wsdl != ""
+rescue
+    puts $!.inspect
+    init_WS
+end
+
+puts "Restarting the WWW service"
+
+FileUtils.rm Dir.glob(File.join('cache/*.lock'))
+
+Merb::Config.setup(
+    :merb_root   => ::File.expand_path(::File.dirname(__FILE__)),
+    :environment => ENV['RACK_ENV']
+)
+
+Merb.environment = Merb::Config[:environment]
+Merb.root        = Merb::Config[:merb_root]
+Merb::BootLoader.run
+
+run Merb::Rack::Application.new
+

data/merb/config/environments/development.rb

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+Merb.logger.info("Loaded DEVELOPMENT Environment...")
+Merb::Config.use { |c|
+  c[:exception_details] = true
+  c[:reload_templates] = true
+  c[:reload_classes] = true
+  c[:reload_time] = 0.5
+  c[:ignore_tampered_cookies] = true
+  c[:log_auto_flush ] = true
+  c[:log_level] = :debug
+
+  c[:log_stream] = STDOUT
+  c[:log_file]   = nil
+  # Or redirect logging into a file:
+  # c[:log_file]  = Merb.root / "log" / "development.log"
+}

data/merb/config/environments/production.rb

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+Merb.logger.info("Loaded PRODUCTION Environment...")
+Merb::Config.use { |c|
+  c[:exception_details] = false
+  c[:reload_classes] = false
+  c[:log_level] = :error
+  
+  c[:log_file]  = Merb.root / "log" / "production.log"
+  # or redirect logger using IO handle
+  # c[:log_stream] = STDOUT
+}

data/merb/config/environments/rake.rb

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+Merb.logger.info("Loaded RAKE Environment...")
+Merb::Config.use { |c|
+  c[:exception_details] = true
+  c[:reload_classes]  = false
+  c[:log_auto_flush ] = true
+
+  c[:log_stream] = STDOUT
+  c[:log_file]   = nil
+  # Or redirect logging into a file:
+  # c[:log_file]  = Merb.root / "log" / "development.log"
+}

data/merb/config/environments/staging.rb

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+Merb.logger.info("Loaded STAGING Environment...")
+Merb::Config.use { |c|
+  c[:exception_details] = false
+  c[:reload_classes]    = false
+  c[:log_level]         = :error
+
+  c[:log_file]  = Merb.root / "log" / "staging.log"
+  # or redirect logger using IO handle
+  # c[:log_stream] = STDOUT
+}

data/merb/config/environments/test.rb

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+Merb.logger.info("Loaded TEST Environment...")
+Merb::Config.use { |c|
+  c[:testing]           = true
+  c[:exception_details] = true
+  c[:log_auto_flush ]   = true
+  # log less in testing environment
+  c[:log_level]         = :error
+
+  #c[:log_file]  = Merb.root / "log" / "test.log"
+  # or redirect logger using IO handle
+  c[:log_stream] = STDOUT
+}

data/merb/config/init.rb

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+# Go to http://wiki.merbivore.com/pages/init-rb
+ 
+# Specify a specific version of a dependency
+# dependency "RedCloth", "> 3.0"
+
+ENV['GEM_HOME']="/home/marq/.ruby/gems/"
+ENV['GEM_PATH']="/home/marq/.ruby/gems/:/var/lib/gems/1.8/"
+
+#  use_orm :none
+use_test :rspec
+use_template_engine :haml
+
+dependency "merb-assets"  
+ 
+require 'compass'
+require 'MARQ'
+require 'fileutils'
+Merb::Config.use do |c|
+  c[:use_mutex] = false
+  c[:session_store] = 'cookie'  # can also be 'memory', 'memcache', 'container', 'datamapper
+  
+  # cookie session store configuration
+  c[:session_secret_key]  = '5d76d9de3239bba8bb00e675f68f24365650a272'  # required for cookie session store
+  c[:session_id_key] = '_marq_session_id' # cookie session id key, defaults to "_session_id"
+
+
+  c[:compass] = {
+    :stylesheets => 'app/stylesheets',
+    :compiled_stylesheets => 'public/stylesheets/'
+  }
+  log_dir = File.join(MARQ.workdir,'merb', 'log')
+  FileUtils.mkdir_p log_dir unless File.exist? log_dir
+  c[:log_file] = File.join(log_dir,'log.txt')
+
+end
+
+require 'redcloth'      
+module RedCloth::Formatters::HTML def br(opts); "\n"; end end
+ 
+Merb::BootLoader.before_app_loads do
+  require 'lib/helper'
+
+ 
+  # This will get executed after dependencies have been loaded but before your app's classes have loaded.
+end
+ 
+Merb::BootLoader.after_app_loads do
+  require 'rand'
+  require 'spreadsheet'
+  require 'MARQ/main'
+  require 'MARQ/annotations'
+  require 'MARQ/rankproduct'
+
+  require 'ruby-yui'
+  # This will get executed after your app's classes have been loaded.
+  #
+
+  CacheHelper.reset_locks
+
+  tmpdir = File.join(MARQ.workdir, 'merb', 'tmp', 'images')
+  FileUtils.mkdir_p(tmpdir) unless File.exist?(tmpdir)
+
+  Merb::Assets::JavascriptAssetBundler.add_callback { |filename| Yui.compress(filename, {:stomp => true, :suffix => ""})} 
+  Merb::Assets::StylesheetAssetBundler.add_callback { |filename| Yui.compress(filename, {:stomp => true, :suffix => ""})} 
+end
+

data/merb/config/rack.rb

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+# use PathPrefix Middleware if :path_prefix is set in Merb::Config
+if prefix = ::Merb::Config[:path_prefix]
+  use Merb::Rack::PathPrefix, prefix
+end
+
+# comment this out if you are running merb behind a load balancer
+# that serves static files
+use Merb::Rack::Static, Merb.dir_for(:public)
+
+# this is our main merb application
+run Merb::Rack::Application.new

data/merb/config/router.rb

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+# Merb::Router is the request routing mapper for the merb framework.
+#
+# You can route a specific URL to a controller / action pair:
+#
+#   match("/contact").
+#     to(:controller => "info", :action => "contact")
+#
+# You can define placeholder parts of the url with the :symbol notation. These
+# placeholders will be available in the params hash of your controllers. For example:
+#
+#   match("/books/:book_id/:action").
+#     to(:controller => "books")
+#   
+# Or, use placeholders in the "to" results for more complicated routing, e.g.:
+#
+#   match("/admin/:module/:controller/:action/:id").
+#     to(:controller => ":module/:controller")
+#
+# You can specify conditions on the placeholder by passing a hash as the second
+# argument of "match"
+#
+#   match("/registration/:course_name", :course_name => /^[a-z]{3,5}-\d{5}$/).
+#     to(:controller => "registration")
+#
+# You can also use regular expressions, deferred routes, and many other options.
+# See merb/specs/merb/router.rb for a fairly complete usage sample.
+
+Merb.logger.info("Compiling routes...")
+Merb::Router.prepare do
+  # RESTful routes
+  # resources :posts
+
+  # This is the default route for /:controller/:action/:id
+  # This is fine for most cases.  If you're heavily using resource-based
+  # routes, you may want to comment/remove this line to prevent
+  # clients from calling your create or destroy actions with a GET
+  #default_routes
+  
+  # Change this for your home page to be available at /
+  match('/images/:image').to(:controller => 'results', :action => 'images')
+  match('/logratios').to(:controller => 'results', :action => 'logratios')
+  match('/ts').to(:controller => 'results', :action => 'ts')
+  match('/compare').to(:controller => 'results', :action => 'compare')
+  match('/experiment_hits').to(:controller => 'results', :action => 'explore_hits')
+  match('/experiment_info').to(:controller => 'results', :action => 'ajax_experiment')
+  match('/annotations').to(:controller => 'results', :action => 'ajax_annotations')
+  match('/partial').to(:controller => 'main', :action => 'ajax_partial')
+  match('/partial').to(:controller => 'main', :action => 'ajax_partial')
+  match('/genes').to(:controller => 'main', :action => 'get_genes')
+  match('/normalize', :method => :post).to(:controller => 'normalize', :action => 'post')
+  match('/normalize').to(:controller => 'normalize', :action => 'index')
+  match('/images/:job').to(:controller => 'results', :action => 'images')
+
+  match('/series/').to(:controller => 'series', :action => 'main')
+  match('/help/').to(:controller => 'help', :action => 'index')
+  match('/help/methods').to(:controller => 'help', :action => 'meth')
+  match('/help/quick').to(:controller => 'help', :action => 'quick')
+
+  match('/:job').to(:controller => 'results', :action => 'main')
+  match('/', :method => :post).to(:controller => 'main', :action =>'post')
+  match('/').to(:controller => 'main', :action =>'index')
+
+
+end