tap-server 0.1.0
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- data/History +5 -0
- data/MIT-LICENSE +19 -0
- data/README +49 -0
- data/cmd/server.rb +34 -0
- data/controllers/app_controller.rb +92 -0
- data/controllers/schema_controller.rb +255 -0
- data/lib/tap/controller.rb +231 -0
- data/lib/tap/server.rb +219 -0
- data/lib/tap/server_error.rb +34 -0
- data/lib/tap/tasks/echo.rb +14 -0
- data/lib/tap/tasks/server.rb +30 -0
- data/public/javascripts/prototype.js +4221 -0
- data/public/javascripts/tap.js +112 -0
- data/public/stylesheets/tap.css +6 -0
- data/tap.yml +0 -0
- data/views/404.erb +9 -0
- data/views/500.erb +7 -0
- data/views/app_controller/index.erb +44 -0
- data/views/app_controller/info.erb +8 -0
- data/views/app_controller/tail.erb +8 -0
- data/views/layout.erb +11 -0
- data/views/schema_controller/config/default.erb +4 -0
- data/views/schema_controller/config/flag.erb +3 -0
- data/views/schema_controller/config/switch.erb +6 -0
- data/views/schema_controller/configurations.erb +27 -0
- data/views/schema_controller/join.erb +4 -0
- data/views/schema_controller/node.erb +47 -0
- data/views/schema_controller/preview.erb +3 -0
- data/views/schema_controller/round.erb +30 -0
- data/views/schema_controller/schema.erb +28 -0
- data/views/tap/tasks/echo/result.html +1 -0
- metadata +109 -0
data/History
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data/MIT-LICENSE
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Copyright (c) 2009, Regents of the University of Colorado.
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Permission is hereby granted, free of charge, to any person obtaining a copy of this
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software and associated documentation files (the "Software"), to deal in the Software
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without restriction, including without limitation the rights to use, copy, modify, merge,
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publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
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to whom the Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all copies or
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substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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OTHER DEALINGS IN THE SOFTWARE.
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data/README
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= {Tap Server}[http://tap.rubyforge.org/tap-server]
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A web interface for {Tap}[http://tap.rubyforge.org/rdoc].
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== Description
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{Tap Server}[http://tap.rubyforge.org/tap-server] provides a web interface for
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Tap tasks. The basic interface allows the construction and execution of
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workflows, rendering of task results, and facilitates distributable
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controllers. The intention is not to make websites for the masses, but rather
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a local interface for individuals and small groups.
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{Tap Server}[http://tap.rubyforge.org/tap-server] is a part of the
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{Tap-Suite}[http://tap.rubyforge.org/tap-suite]. Check out these links for
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documentation, development, and bug tracking.
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* Website[http://tap.rubyforge.org]
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* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/9908-tap-task-application/tickets]
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* Github[http://github.com/bahuvrihi/tap/tree/master]
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* {Google Group}[http://groups.google.com/group/ruby-on-tap]
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== Usage
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To get a peek, use the command:
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% tap server
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Then go to the url 'localhost:8080'. Currently tap-server is in alpha and
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should not be considered stable.
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== Installation
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Tap Server is available as a gem on RubyForge[http://rubyforge.org/projects/tap]. Use:
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% gem install tap-server
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Tap requires an updated version of RubyGems[http://docs.rubygems.org/]
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(>= 1.2.0). To check the version and update RubyGems:
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% gem --version
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% gem --update system
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== Info
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Copyright (c) 2009, Regents of the University of Colorado.
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Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/]
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Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
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Licence:: {MIT-Style}[link:files/MIT-LICENSE.html]
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data/cmd/server.rb
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# tap server {options}
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#
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# Initializes a tap server.
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require 'tap'
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require 'tap/server'
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env = Tap::Env.instance
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app = Tap::App.instance
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#
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# handle options
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#
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config_path = nil
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opts = ConfigParser.new do |opts|
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opts.separator ""
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opts.separator "options:"
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opts.add(Tap::Server.configurations)
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# add option to print help
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opts.on("-h", "--help", "Show this message") do
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puts Lazydoc.usage(__FILE__)
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puts opts
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exit
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end
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end
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# parse!
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argv = opts.parse(ARGV)
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server = Tap::Server.new(env, app, opts.config)
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cookie_server = Rack::Session::Pool.new(server)
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Rack::Handler::WEBrick.run(cookie_server, :Port => server.port)
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require 'tap/controller'
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require 'rack/mime'
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require 'time'
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class AppController < Tap::Controller
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set :default_layout, 'layout.erb'
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def call(env)
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# serve public files before actions
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server = env['tap.server'] ||= Tap::Server.new
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if path = server.public_path(env['PATH_INFO'])
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content = File.read(path)
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headers = {
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"Last-Modified" => [File.mtime(path).httpdate],
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"Content-Type" => [Rack::Mime.mime_type(File.extname(path), 'text/plain')],
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"Content-Length" => [content.size.to_s]
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}
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[200, headers, [content]]
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else
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super
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end
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end
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def index
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env_names = {}
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server.env.minimap.each do |name, environment|
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env_names[environment] = name
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end
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render('index.erb', :locals => {:env => server.env, :env_names => env_names}, :layout => true)
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end
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def info
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if request.post?
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app.info
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else
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render('info.erb', :locals => {:update => true, :content => app.info}, :layout => true)
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end
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end
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#--
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# Currently tail is hard-coded to tail the server log only.
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def tail(id=nil)
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begin
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path = app.subpath(:log, 'server.log')
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raise unless File.exists?(path)
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rescue
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raise Tap::ServerError.new("invalid path", 404)
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end
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pos = request['pos'].to_i
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if pos > File.size(path)
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raise Tap::ServerError.new("tail position out of range (try update)", 500)
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end
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content = File.open(path) do |file|
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file.pos = pos
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file.read
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end
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if request.post?
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content
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else
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render('tail.erb', :locals => {
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:id => id,
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:path => File.basename(path),
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:update => true,
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:content => content
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}, :layout => true)
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end
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end
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def run
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Thread.new { app.run }
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redirect("/app/tail")
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end
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def stop
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app.stop
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redirect("/app/info")
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end
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def terminate
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app.terminate
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redirect("/app/info")
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end
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def help(key=nil)
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end
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end
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require 'tap/controller'
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class SchemaController < Tap::Controller
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set :default_layout, 'layout.erb'
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# Initializes a new schema and redirects to display.
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def index
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id = initialize_schema
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redirect("/schema/display/#{id}")
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end
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# Loads the schema indicated by id and renders 'schema.erb' with the default
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# layout.
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def display(id)
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schema = load_schema(id)
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render 'schema.erb', :locals => {
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:id => id,
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:schema => schema
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}, :layout => true
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end
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# Updates the specified schema with the request parameters. Update forwards
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# the request to the action ('add' or 'remove') specified in the action
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# parameter.
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def update(id)
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case request['action']
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when 'add' then add(id)
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when 'remove' then remove(id)
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when 'echo' then echo
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else raise Tap::ServerError, "unknown action: #{request['action']}"
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end
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end
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# Adds nodes or joins to the schema. Parameters:
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#
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# nodes[]:: An array of nodes to add to the schema. Each entry is split using
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# Shellwords to yield an argv; the argv initializes the node. The
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# index of each new node is added to targets[].
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# sources[]:: An array of source node indicies used to create a join.
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# targets[]:: An array of target node indicies used to create a join (note
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# the indicies of new nodes are added to targets).
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#
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# Add creates and pushes new nodes onto schema as specified in nodes, then
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# creates joins between the sources and targets. The join class is inferred
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# by Utils.infer_join; if no join can be inferred the join class is
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# effectively nil, and consistent with that, the node output for sources
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# and the node input for targets is set to nil.
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#
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# === Notes
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#
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# The nomenclature for source and target is relative to the join, and may
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# seem backwards for the node (ex: 'sources[]=0&targets[]=1' makes a join
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# like '0:1')
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#
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def add(id)
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unless request.post?
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raise Tap::ServerError, "add must be performed with post"
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end
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round = (request['round'] || 0).to_i
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outputs = (request['outputs[]'] || []).collect {|index| index.to_i }
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inputs = (request['inputs[]'] || []).collect {|index| index.to_i }
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nodes = request['nodes[]'] || []
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load_schema(id) do |schema|
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nodes.each do |arg|
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next unless arg && !arg.empty?
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outputs << schema.nodes.length
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schema.nodes << Tap::Support::Node.new(Shellwords.shellwords(arg), round)
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end
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if inputs.empty? || outputs.empty?
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inputs.each {|index| schema[index].output = nil }
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outputs.each {|index| schema[index].input = round }
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else
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# temporary
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if inputs.length > 1 && outputs.length > 1
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raise "multi-way join specified"
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end
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schema.set(Tap::Support::Join, inputs, outputs)
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end
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end
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redirect("/schema/display/#{id}")
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end
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# Removes nodes or joins from the schema. Parameters:
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#
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# sources[]:: An array of source node indicies to remove.
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# targets[]:: An array of target node indicies to remove.
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#
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# Normally remove sets the node.output for each source to nil and the
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# node.input for each target to nil. However, if a node is indicated in
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# both sources and targets AND it has no join input/output, then it will
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# be removed.
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#
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# === Notes
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#
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# The nomenclature for source and target is relative to the join, and may
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# seem backwards for the node (ex: for the sequence '0:1:2', 'targets[]=1'
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# breaks the join '0:1' while 'sources[]=1' breaks the join '1:2'.
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#
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def remove(id)
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unless request.post?
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raise Tap::ServerError, "remove must be performed with post"
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end
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round = (request['round'] || 0).to_i
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outputs = (request['outputs[]'] || []).collect {|index| index.to_i }
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inputs = (request['inputs[]'] || []).collect {|index| index.to_i }
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+
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load_schema(id) do |schema|
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# Remove joins. Removed indicies are popped to ensure
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# that if a join was removed the node will not be.
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outputs.delete_if do |index|
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next unless node = schema.nodes[index]
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if node.input_join
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node.input = round
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true
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else
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false
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end
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end
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127
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+
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128
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inputs.delete_if do |index|
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next unless node = schema.nodes[index]
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130
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if node.output_join
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node.output = nil
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true
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else
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false
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135
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end
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136
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end
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137
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+
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# Remove nodes. Setting a node to nil causes it's removal during
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# compact; orphaned joins are removed during compact as well.
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140
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(inputs & outputs).each do |index|
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schema.nodes[index] = nil
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142
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+
end
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143
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+
end
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144
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+
|
145
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redirect("/schema/display/#{id}")
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146
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+
end
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147
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+
|
148
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def submit(id)
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149
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case request['action']
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150
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when 'save' then save(id)
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when 'preview' then preview(id)
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when 'echo' then echo
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when 'run'
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dump_schema(id, schema)
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run(id)
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+
else raise Tap::ServerError, "unknown action: #{request['action']}"
|
157
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+
end
|
158
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+
end
|
159
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+
|
160
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def save(id)
|
161
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+
unless request.post?
|
162
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+
raise Tap::ServerError, "submit must be performed with post"
|
163
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+
end
|
164
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+
|
165
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dump_schema(id, schema)
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redirect("/schema/display/#{id}")
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+
end
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+
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def preview(id)
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+
response.headers['Content-Type'] = 'text/plain'
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render('preview.erb', :locals => {:id => id, :schema => schema})
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+
end
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+
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+
def run(id)
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+
unless request.post?
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+
raise Tap::ServerError, "run must be performed with post"
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+
end
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+
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+
# it would be nice to someday put all this on a separate thread...
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+
schema = load_schema(id)
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+
tasks = server.env.tasks
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+
schema.build(app) do |(key, *args)|
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+
if const = tasks.search(key)
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+
const.constantize.parse(args, app) do |help|
|
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+
raise "help not implemented"
|
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|
+
#redirect("/app/help/#{key}")
|
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|
+
end
|
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|
+
else
|
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|
+
raise ArgumentError, "unknown task: #{key}"
|
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+
end
|
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|
+
end
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+
|
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Thread.new { app.run }
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redirect("/app/tail")
|
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+
end
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+
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+
protected
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+
|
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|
+
# Parses a Tap::Support::Schema from the request.
|
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+
def schema
|
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|
+
argv = request['argv[]'] || []
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|
+
argv.delete_if {|arg| arg.empty? }
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|
+
Tap::Support::Schema.parse(argv)
|
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|
+
end
|
205
|
+
|
206
|
+
def initialize_schema
|
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|
+
current = app.glob(:schema, "*").collect {|path| File.basename(path).chomp(".yml") }
|
208
|
+
|
209
|
+
id = random_key(current.length)
|
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|
+
while current.include?(id)
|
211
|
+
id = random_key(current.length)
|
212
|
+
end
|
213
|
+
|
214
|
+
dump_schema(id, schema)
|
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|
+
id
|
216
|
+
end
|
217
|
+
|
218
|
+
def load_schema(id)
|
219
|
+
unless path = app.filepath(:schema, "#{id}.yml")
|
220
|
+
raise ServerError, "no schema for id: #{id}"
|
221
|
+
end
|
222
|
+
schema = Tap::Support::Schema.load_file(path)
|
223
|
+
|
224
|
+
if block_given?
|
225
|
+
result = yield(schema)
|
226
|
+
dump_schema(id, schema)
|
227
|
+
result
|
228
|
+
else
|
229
|
+
schema
|
230
|
+
end
|
231
|
+
end
|
232
|
+
|
233
|
+
def dump_schema(id, schema=nil)
|
234
|
+
app.prepare(:schema, "#{id}.yml") do |file|
|
235
|
+
file << schema.dump.to_yaml if schema
|
236
|
+
end
|
237
|
+
end
|
238
|
+
|
239
|
+
def instantiate(*argv)
|
240
|
+
key = argv.shift
|
241
|
+
tasc = server.env.tasks.search(key).constantize
|
242
|
+
tasc.parse(argv)
|
243
|
+
end
|
244
|
+
|
245
|
+
# helper to echo requests back... good for debugging
|
246
|
+
def echo # :nodoc:
|
247
|
+
"<pre>#{request.params.to_yaml}</pre>"
|
248
|
+
end
|
249
|
+
|
250
|
+
# Generates a random integer key.
|
251
|
+
def random_key(length) # :nodoc:
|
252
|
+
length = 1 if length < 1
|
253
|
+
rand(length * 10000).to_s
|
254
|
+
end
|
255
|
+
end
|
@@ -0,0 +1,231 @@
|
|
1
|
+
require 'tap/server'
|
2
|
+
autoload(:ERB, 'erb')
|
3
|
+
|
4
|
+
module Tap
|
5
|
+
|
6
|
+
# === Declaring Actions
|
7
|
+
# By default all public methods in subclasses are declared as actions. You
|
8
|
+
# can declare a private or protected method as an action by:
|
9
|
+
#
|
10
|
+
# * manually adding it directly to actions
|
11
|
+
# * defining it as a public method and then call private(:method) or protected(:method)
|
12
|
+
#
|
13
|
+
# Similarly, public method can be made non-action by actions by:
|
14
|
+
#
|
15
|
+
# * manually deleting it from actions
|
16
|
+
# * define it private or protected then call public(:method)
|
17
|
+
#
|
18
|
+
class Controller
|
19
|
+
class << self
|
20
|
+
|
21
|
+
# Initialize instance variables on the child and inherit as necessary.
|
22
|
+
def inherited(child) # :nodoc:
|
23
|
+
super
|
24
|
+
child.set(:actions, actions.dup)
|
25
|
+
child.set(:middleware, middleware.dup)
|
26
|
+
child.set(:default_layout, default_layout)
|
27
|
+
child.set(:define_action, true)
|
28
|
+
end
|
29
|
+
|
30
|
+
# An array of methods that can be called as actions. Actions must be
|
31
|
+
# stored as symbols. Actions are inherited.
|
32
|
+
attr_reader :actions
|
33
|
+
|
34
|
+
# An array of Rack middleware that will be applied when handing requests
|
35
|
+
# through the class call method. Middleware is inherited.
|
36
|
+
attr_reader :middleware
|
37
|
+
|
38
|
+
# The default layout rendered when the render option :layout is true.
|
39
|
+
attr_reader :default_layout
|
40
|
+
|
41
|
+
# The base path prepended to render paths (ie render(<path>) renders
|
42
|
+
# <templates_dir/name/path>).
|
43
|
+
def name
|
44
|
+
@name ||= to_s.underscore
|
45
|
+
end
|
46
|
+
|
47
|
+
# Adds the specified middleware. Middleware classes are initialized
|
48
|
+
# with the specified args and block, and applied to in the order in
|
49
|
+
# which they are declared (ie first use processes requests first).
|
50
|
+
#
|
51
|
+
# Middleware is applied through the class call method, and on a per-call
|
52
|
+
# basis... middleware like Rack::Session::Pool that is supposed to
|
53
|
+
# persist for the life of an application will not work properly.
|
54
|
+
#
|
55
|
+
# Middleware is inherited.
|
56
|
+
def use(middleware, *args, &block)
|
57
|
+
@middleware << [middleware, args, block]
|
58
|
+
end
|
59
|
+
|
60
|
+
# Instantiates self and performs call. Middleware is applied in the
|
61
|
+
# order in which it was declared.
|
62
|
+
#--
|
63
|
+
# Note that middleware needs to be initialized in reverese, so that
|
64
|
+
# the first declared middleware runs first.
|
65
|
+
def call(env)
|
66
|
+
app = new
|
67
|
+
middleware.reverse_each do |(m, args, block)|
|
68
|
+
app = m.new(app, *args, &block)
|
69
|
+
end
|
70
|
+
app.call(env)
|
71
|
+
end
|
72
|
+
|
73
|
+
# Sets an instance variable for self, short for:
|
74
|
+
#
|
75
|
+
# instance_variable_set(:@attribute, input)
|
76
|
+
#
|
77
|
+
# Typically only these variables should be set:
|
78
|
+
#
|
79
|
+
# actions:: sets actions
|
80
|
+
# name:: the name of the controller
|
81
|
+
# default_layout:: the default layout (used by render)
|
82
|
+
#
|
83
|
+
def set(variable, input)
|
84
|
+
instance_variable_set("@#{variable}", input)
|
85
|
+
end
|
86
|
+
|
87
|
+
protected
|
88
|
+
|
89
|
+
# Overridden so that if declare_action is set, new methods
|
90
|
+
# are added to actions.
|
91
|
+
def method_added(sym) # :nodoc:
|
92
|
+
actions << sym if @define_action
|
93
|
+
super
|
94
|
+
end
|
95
|
+
|
96
|
+
# Turns on declare_action when changing method context.
|
97
|
+
def public(*symbols) # :nodoc:
|
98
|
+
@define_action = true if symbols.empty?
|
99
|
+
super
|
100
|
+
end
|
101
|
+
|
102
|
+
# Turns off declare_action when changing method context.
|
103
|
+
def protected(*symbols) # :nodoc:
|
104
|
+
@define_action = false if symbols.empty?
|
105
|
+
super
|
106
|
+
end
|
107
|
+
|
108
|
+
# Turns off declare_action when changing method context.
|
109
|
+
def private(*symbols) # :nodoc:
|
110
|
+
@define_action = false if symbols.empty?
|
111
|
+
super
|
112
|
+
end
|
113
|
+
end
|
114
|
+
|
115
|
+
set :actions, []
|
116
|
+
set :middleware, []
|
117
|
+
set :default_layout, nil
|
118
|
+
set :define_action, false
|
119
|
+
|
120
|
+
include Rack::Utils
|
121
|
+
|
122
|
+
# Accesses the 'tap.server' specified in env, set during call.
|
123
|
+
attr_accessor :server
|
124
|
+
|
125
|
+
# A Rack::Request wrapping env, set during call.
|
126
|
+
attr_accessor :request
|
127
|
+
|
128
|
+
# A Rack::Response. If the action returns a string, it will be written to
|
129
|
+
# response and response will be returned by call. Otherwise, call returns
|
130
|
+
# the action result and response is ignored.
|
131
|
+
attr_accessor :response
|
132
|
+
|
133
|
+
# Initializes a new instance of self. The input attributes are reset by
|
134
|
+
# call and are only provided for convenience during testing.
|
135
|
+
def initialize(server=nil, request=nil, response=nil)
|
136
|
+
@server = server
|
137
|
+
@request = request
|
138
|
+
@response = response
|
139
|
+
end
|
140
|
+
|
141
|
+
def call(env)
|
142
|
+
@server = env['tap.server'] || Tap::Server.new
|
143
|
+
@request = Rack::Request.new(env)
|
144
|
+
@response = Rack::Response.new
|
145
|
+
|
146
|
+
# route to an action
|
147
|
+
blank, action, *args = request.path_info.split("/").collect {|arg| unescape(arg) }
|
148
|
+
action = "index" if action == nil || action.empty?
|
149
|
+
|
150
|
+
unless self.class.actions.include?(action.to_sym)
|
151
|
+
raise ServerError.new("404 Error: page not found", 404)
|
152
|
+
end
|
153
|
+
|
154
|
+
result = send(action, *args)
|
155
|
+
if result.kind_of?(String)
|
156
|
+
response.write result
|
157
|
+
response.finish
|
158
|
+
else
|
159
|
+
result
|
160
|
+
end
|
161
|
+
end
|
162
|
+
|
163
|
+
def render(path, options={})
|
164
|
+
options, path = path, nil if path.kind_of?(Hash)
|
165
|
+
|
166
|
+
# lookup template
|
167
|
+
template_path = case
|
168
|
+
when options.has_key?(:template)
|
169
|
+
server.template_path(options[:template])
|
170
|
+
else
|
171
|
+
server.template_path("#{self.class.name}/#{path}")
|
172
|
+
end
|
173
|
+
|
174
|
+
unless template_path
|
175
|
+
raise "could not find template for: #{path}"
|
176
|
+
end
|
177
|
+
|
178
|
+
# render template
|
179
|
+
template = server.content(template_path)
|
180
|
+
content = render_erb(template, options)
|
181
|
+
|
182
|
+
# render layout
|
183
|
+
layout = options[:layout]
|
184
|
+
layout = self.class.default_layout if layout == true
|
185
|
+
if layout
|
186
|
+
render(:template => layout, :locals => {:content => content})
|
187
|
+
else
|
188
|
+
content
|
189
|
+
end
|
190
|
+
end
|
191
|
+
|
192
|
+
def render_erb(template, options={})
|
193
|
+
# assign locals to the render binding
|
194
|
+
# this almost surely may be optimized...
|
195
|
+
locals = options[:locals]
|
196
|
+
binding = empty_binding
|
197
|
+
|
198
|
+
locals.each_pair do |key, value|
|
199
|
+
@assignment_value = value
|
200
|
+
eval("#{key} = remove_instance_variable(:@assignment_value)", binding)
|
201
|
+
end if locals
|
202
|
+
|
203
|
+
ERB.new(template, nil, "<>").result(binding)
|
204
|
+
end
|
205
|
+
|
206
|
+
# Redirects to the specified uri.
|
207
|
+
def redirect(uri, status=302, headers={}, body="")
|
208
|
+
response.status = status
|
209
|
+
response.headers.merge!(headers)
|
210
|
+
response.body = body
|
211
|
+
|
212
|
+
response['Location'] = uri
|
213
|
+
response.finish
|
214
|
+
end
|
215
|
+
|
216
|
+
# Returns a session hash.
|
217
|
+
def session
|
218
|
+
request.env['rack.session'] ||= {}
|
219
|
+
end
|
220
|
+
|
221
|
+
# Returns the app for the current session.
|
222
|
+
def app
|
223
|
+
server.app(session[:id] ||= server.initialize_session)
|
224
|
+
end
|
225
|
+
|
226
|
+
# Generates an empty binding to self without any locals assigned.
|
227
|
+
def empty_binding # :nodoc:
|
228
|
+
binding
|
229
|
+
end
|
230
|
+
end
|
231
|
+
end
|