rbbt-views 0.1.0

data/lib/rbbt/workflow/rest.rb

@@ -0,0 +1,437 @@
+require 'rbbt'
+require 'rbbt/workflow'
+require 'rbbt/util/log'
+require 'compass'
+require 'haml'
+require 'json'
+
+require 'sinatra/authorization'
+
+require 'rbbt/workflow/rest/util.rb'
+require 'rbbt/workflow/rest/render.rb'
+require 'rbbt/workflow/rest/auth.rb'
+
+module WorkflowREST
+  extend Resource
+
+  class << self
+    attr_accessor :workflows
+    self
+  end
+  self.workflows = []
+
+  def self.setup
+    configure do
+      Compass.add_project_configuration(WorkflowREST.share.views.compass["compass.config"].find.dup.to_s)
+    end
+
+    Sinatra.module_eval do
+      helpers Sinatra::SinatraRbbt
+      enable :sessions
+
+      before do
+        @file_cache = {}
+        @result_cache = {}
+      end
+
+      after do
+        @file_cache.clear
+        @result_cache.clear
+      end
+
+      helpers do
+        def authorization_realm
+          "Workflow Explorer"
+        end
+
+        def authorize(login, password)
+          login == "miki" && password == "miki"
+        end
+
+        def check_user(user)
+          login_required
+          request.env['REMOTE_USER'] == user || throw(:halt, [ 401, 'Authorization Required' ])
+        end
+      end
+
+    end
+
+    set :public, Sinatra::SinatraRbbt.locate_file(nil, nil, 'public/').find
+
+    get '/stylesheets/:name.css' do
+      file = locate_file(nil, nil, File.join("compass", params[:name] + '.sass'))
+      css = Persist.persist("Stylesheet:#{file}", :string, :persist => ENV["RACK_ENV"].to_s == 'production', :dir => 'cache') do
+        renderer = Sass::Engine.new(file.read)
+        renderer.render.to_s
+      end
+      content_type 'text/css', :charset => 'utf-8'
+      css
+    end
+
+    get '/js/:name.js' do
+      content_type 'text/css', :charset => 'utf-8'
+      file = locate_file(nil, nil, File.join("js", params[:name] + '.js'))
+      file.read
+    end
+
+    get '/entity/:type/:entity' do
+      type = params[:type]
+
+      entity_render(type, params)
+    end
+
+  end
+
+  def self.add_task(workflow, task_name, type = nil)
+    type ||= :synchronous
+    task_name = task_name.to_s
+    workflow_name = workflow.to_s
+
+    # MOVE!!!!
+    get File.join("/plugins", workflow_name, "*") do
+      file = params[:splat].first
+      send_file Sinatra::SinatraRbbt.locate_file(workflow, nil, 'plugins/' + file)
+    end
+
+    # context info
+    delete File.join("/context", workflow_name, ":task") do
+      task, jobname = params.values_at :task
+      del_context_job(workflow, task)
+      true
+    end
+
+    post File.join("/context", workflow_name, ":task", ":jobname") do
+      task, jobname = params.values_at :task, :jobname
+      add_context_job(workflow, task, jobname)
+      true
+    end
+
+    # task info
+    get File.join("/", workflow_name, task_name, 'info') do
+
+      visualization_parameters = get_visualization_parameters(params)
+      task_info = workflow.task_info(task_name)
+
+      case
+      when visualization_parameters[:_format] == "json"
+        task_info.to_json
+      when visualization_parameters[:_format] == "raw"
+        task_info.collect{|k,v| [k,v] * "\t"} * "\n"
+      when visualization_parameters[:_format] == "html"
+        workflow_render(workflow, task_name, "task_info", workflow.task_info(task_name).merge(visualization_parameters).merge(:task_info => task_info))
+      end
+    end
+
+    # task jobs
+    get File.join("/", workflow_name, task_name, 'jobs') do
+      visualization_parameters = get_visualization_parameters(params)
+      task_info = workflow.task_info(task_name)
+
+      authorize!
+
+      job_list = workflow.jobs(task_name, user + "/").collect{|jobname| File.basename(jobname)}
+
+      workflow_render(workflow, task_name, "job_list", visualization_parameters.merge(:workflow => workflow, :task_name => task_name, :job_list => job_list))
+    end
+
+
+    # task form or exec
+    get File.join("/", workflow_name, task_name) do
+
+      visualization_parameters = get_visualization_parameters(params)
+      inputs = get_inputs(workflow, task_name, params)
+
+      case
+        # direct exection when job has all paramteres
+      when (type == :exec and has_all_inputs(workflow, task_name, inputs))
+        result = workflow.job(task_name, "EXEC", inputs.dup).exec
+        result = paginate(result, params[:_page]) if params.include? :_page
+
+        workflow_render_result(workflow, task_name, result, visualization_parameters.merge(:inputs => inputs))
+
+        # direct job issuing and redirection when job has all paramteres
+      when has_all_inputs(workflow, task_name, inputs)
+        params[:jobname] = "WWW" unless params.include? :jobname or params.include? "jobname"
+
+        jobname = get_jobname(params)
+        real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+        job = workflow.job(task_name, real_jobname, inputs.dup)
+
+        if type.to_sym == :synchronous
+          job.run
+        else
+          job.fork
+        end
+
+        redirection = to(File.join("/", workflow.to_s, task_name, File.basename(job.path)))
+
+        redirection = add_param(redirection, :_format, visualization_parameters[:_format]) if visualization_parameters[:_format] != "html"
+        redirection = add_param(redirection, :_page, visualization_parameters[:_page]) if visualization_parameters[:_page] != nil
+        redirection = add_param(redirection, :_size, visualization_parameters[:_size]) if visualization_parameters[:_size] != nil
+        redirection = add_param(redirection, :_layout, visualization_parameters[:_layout]) unless visualization_parameters[:_layout]
+
+        redirect redirection
+      else
+        workflow_render(workflow, task_name, "form", workflow.task_info(task_name).merge(visualization_parameters))
+      end
+    end
+
+    # job for task form post
+    post File.join("/", workflow_name, task_name) do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+      inputs = get_inputs(workflow, task_name, params)
+
+      case type.to_sym
+
+      when :exec
+        result = workflow.job(task_name, real_jobname, inputs.dup).exec
+        workflow_render_result(workflow, task_name, result, visualization_parameters.merge(:inputs => inputs))
+
+      when :synchronous, :asynchronous
+        job = workflow.job(task_name, real_jobname, inputs)
+
+        if type.to_sym == :synchronous
+          job.run
+        else
+          job.fork
+        end
+
+        return job.name if visualization_parameters[:_format] == "json"
+
+        redirection = to(File.join("/", workflow.to_s, task_name, job.name.sub(/.*\//,'')))
+
+        redirection = add_param(redirection, :_format, visualization_parameters[:_format]) if visualization_parameters[:_format] != "html"
+        redirection = add_param(redirection, :_page, visualization_parameters[:_page]) if visualization_parameters[:_page] != nil
+        redirection = add_param(redirection, :_size, visualization_parameters[:_size]) if visualization_parameters[:_size] != nil
+        redirection = add_param(redirection, :_layout, visualization_parameters[:_layout]) unless visualization_parameters[:_layout]
+
+        redirect redirection
+      end
+    end
+
+    # job results
+    get File.join("/", workflow.to_s, task_name, ":jobname") do
+      jobname = get_jobname(params)
+
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+      inputs = get_inputs(workflow, task_name, params)
+
+      session[:jobname] = jobname
+
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      case
+
+        # ERROR
+      when step.error?
+
+        if visualization_parameters[:_format] == "html"
+          content_type "text/html"
+          status 500
+          return workflow_render(workflow, task_name, "error", workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
+        else
+          status 500
+          content_type "text/plain"
+          step.messages.last
+        end
+
+        # NOT DONE
+      when (not step.done?)
+
+        if visualization_parameters[:_format] == "html"
+          content_type "text/html"
+          status 202
+          @rbbt_refresh = 30 unless step.error?
+          return workflow_render(workflow, task_name, "wait", workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs]))
+        else
+          status 202
+          step.status
+        end
+
+        # DONE
+      else
+
+        case
+        when visualization_parameters[:_format] == "html"
+          result = step.load
+          workflow_render_result(workflow, task_name, result, workflow.task_info(task_name).merge(visualization_parameters).merge(:jobname => jobname, :step => step, :inputs => step.info[:inputs], :result => result))
+
+        when visualization_parameters[:_format] == "json"
+          content_type "application/json"
+          result = step.load
+          result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
+          result.to_json
+
+        else
+          content_type "text/plain"
+          result = step.load
+          result = paginate(result, visualization_parameters[:_page]) if visualization_parameters.include? "_page"
+          result.to_s
+        end
+
+      end
+    end
+
+    # job info
+    get File.join("/", workflow.to_s, task_name, ":jobname", 'info') do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      info = step.info
+
+      case
+      when visualization_parameters[:_format] == "json"
+        content_type "application/json"
+        info.to_json
+      when visualization_parameters[:_format] == "raw"
+        info.collect{|k,v| [k,v] * "\t"} * "\n"
+      when visualization_parameters[:_format] == "html"
+        workflow_render(workflow, task_name, "info", visualization_parameters.merge(:info => info))
+      end
+    end
+
+    # job dependencies
+    get File.join("/", workflow.to_s, task_name, ":jobname", 'dependencies') do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      dependencies = step.info[:dependencies]
+
+      case
+      when visualization_parameters[:_format] == "json"
+        content_type "application/json"
+        depencencies.to_json
+      when visualization_parameters[:_format] == "raw"
+        dependencies.collect{|task, job| [task, job] * "\t"} * "\n"
+      when visualization_parameters[:_format] == "html"
+        workflow_render(workflow, task_name, "dependencies", visualization_parameters.merge(:dependencies => dependencies, :workflow => workflow, :task_name => task_name, :jobname => jobname))
+      end
+    end
+
+    # job files
+    get File.join("/", workflow.to_s, task_name, ":jobname", 'files') do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      files = step.files
+
+      case
+      when visualization_parameters[:_format] == "json"
+        content_type "application/json"
+        files.to_json
+      when visualization_parameters[:_format] == "raw"
+        files * "\n"
+      when visualization_parameters[:_format] == "html"
+        workflow_render(workflow, task_name, "files", visualization_parameters.merge(:files => files, :workflow => workflow, :task_name => task_name, :jobname => jobname))
+      end
+    end
+
+    # job file
+    get File.join("/", workflow.to_s, task_name, ":jobname", 'file', '*') do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      filename = params[:splat].first
+      filepath = step.file(filename)
+
+      file = step.load_file(filename)
+
+      case
+      when visualization_parameters[:_format] == "json"
+        content_type "application/json"
+        file.to_json
+      else
+        begin
+          content_type `file --mime -b #{filepath}`
+        rescue
+          if filepath =~ /.xlsx?/
+            content_type "application/vnd.ms-excel"
+          end
+        end
+
+        case
+        when Array === file
+          file * "\n"
+        when TSV === file
+          file.to_s
+        when Hash === file
+          file.collect{|*p| p * "\t"} * "\n"
+        else
+          file.to_s
+        end
+      end
+    end
+
+    # delete job
+    delete File.join("/", workflow.to_s, task_name, ":jobname") do
+      jobname = get_jobname(params)
+      real_jobname = authorized? ? File.join(user, jobname) : jobname
+
+      visualization_parameters = get_visualization_parameters(params)
+      step = workflow.load_id(File.join(task_name, real_jobname))
+
+      step.clean
+    end
+  end
+
+
+  def self.add_workflows(*workflows)
+    self.workflows.concat workflows
+    self.workflows.uniq!
+    get '/' do
+      visualization_parameters = get_visualization_parameters(params)
+      workflow_render(nil, nil, "workflow_list", visualization_parameters.merge(:workflows => WorkflowREST.workflows))
+    end
+
+
+    WorkflowREST.workflows.each do |workflow|
+      get File.join('/', workflow.to_s) do
+        visualization_parameters = get_visualization_parameters(params)
+
+        tasks = workflow.exec_exports + workflow.synchronous_exports + workflow.asynchronous_exports
+        if visualization_parameters[:_format] and visualization_parameters[:_format].to_sym == :json
+          tasks.to_json
+        else
+          workflow_render(workflow, nil, "task_list", visualization_parameters.merge(:workflow => workflow, :tasks => tasks))
+        end
+      end
+
+      workflow.asynchronous_exports.each do |name|
+        WorkflowREST.add_task workflow, name, :asynchronous
+      end
+
+      workflow.synchronous_exports.each do |name|
+        WorkflowREST.add_task workflow, name, :synchronous
+      end
+
+      workflow.exec_exports.each do |name|
+        WorkflowREST.add_task workflow, name, :exec
+      end
+
+    end
+
+  end
+
+end

data/share/views/compass/_base.sass

@@ -0,0 +1,19 @@
+$blueprint_grid_columns: 16
+$blueprint_grid_width: 40px
+$blueprint_grid_margin: 10px
+
+$font_color: #333
+$blueprint-font-size: 14px
+
+@import compass/reset
+@import compass/utilities
+@import blueprint
+@import "blueprint/buttons"
+@import "compass/css3/inline-block"
+@import "blueprint/form"
+@import "blueprint/grid"
+@import "blueprint/typography"
+@import "compass/utilities/general/clearfix"
+@import "compass/css3/border-radius"
+
++blueprint-typography

data/share/views/compass/app.sass

@@ -0,0 +1,103 @@
+@import "main"
+@import "form"
+
+body
+  margin: 10px
+  font-size: 12px
+  width: auto
+
+span.short_task_description
+  display: block
+  color: gray
+
+.embedded
+  margin: 0
+  padding: 0
+  &.reloading
+    span.status
+      font-size: 2em
+      color: gray
+
+#header 
+  background-color: #F2F2F2
+  h1 
+    font-size: 15px
+    a
+      text-decoration: none
+      color: blue
+    span.login
+      float: right
+
+#menu
+  font-size: 0.9em
+  overflow: auto
+  overflow-x: hidden
+  +column(5)
+  ul
+    +clean_list
+    li
+      display: block
+        
+  .workflow_menu
+    margin-bottom: 20px
+
+ul.context_control
+  +clean_list(true)
+  height: 2em
+  li
+    float: left
+    padding: 3px
+    margin-left: 5px
+
+
+ul.job_control
+  +clean_list(true)
+  height: 2em
+  li
+    float: right
+    padding: 3px
+    margin-right: 15px
+
+#content
+  +column(19)
+  #main
+    width: auto
+    padding: 10px
+    &.contracted
+      +border_radius(4px, 4px)
+      overflow: auto
+      border: solid 1px gray
+  #details_controls
+    ul
+      +clean_list
+      li
+        margin: 0px
+        padding: 0px
+      a
+        +subtle_link(gray)
+  #details
+    +border_radius(4px, 4px)
+    padding: 10px
+    height: 200px
+    border: solid 1px gray
+    background-color: #F2F2F2
+    overflow: auto
+    &.expanded
+      height: auto
+      overflow: none
+
+  #other_task_jobs
+    +column(5)
+    float: right
+
+#footer
+  margin-top: 20px
+  color: orange
+
+span.input_name
+  font-weight: bold
+
+table tfoot 
+  input
+    &.pnum, &.psize
+      width: 3em

data/share/views/compass/compass.config

@@ -0,0 +1,33 @@
+require 'rbbt/workflow/rest'
+
+if defined?(Sinatra)
+  # This is the configuration to use when running within sinatra
+  project_path = Sinatra::Application.root
+  environment = :development
+else
+  # this is the configuration to use when running within the compass command line tool.
+  css_dir = File.join 'public', 'stylesheets'
+  relative_assets = true
+  environment = :production
+end
+
+Sass::Engine::DEFAULT_OPTIONS[:load_paths].tap do |load_paths| 
+  load_paths << WorkflowREST.views.compass.find(:lib, Sinatra::Application.root).to_s 
+  Workflow.workflows.each do |workflow|
+    load_paths << WorkflowREST.www.views.compass.find(:lib, workflow.libdir).to_s 
+  end
+  load_paths << WorkflowREST.share.views.compass.find(:lib).to_s 
+
+  load_paths << "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/compass/stylesheets"
+  load_paths << "#{Gem.loaded_specs['compass'].full_gem_path}/frameworks/blueprint/stylesheets"
+end
+
+# This is common configuration
+sass_dir = WorkflowREST.share.views.compass.find(:lib, Sinatra::Application.root).to_s
+cache_dir = WorkflowREST.var.cache.sass.find
+images_dir = File.join 'public', 'images'
+http_path = "/"
+http_images_path = "/images"
+http_stylesheets_path = "/stylesheets"
+
+# vim: ft=ruby

data/share/views/compass/form.sass

@@ -0,0 +1,23 @@
+span.form_title
+  display: block
+  font-size: 2em
+  margin-bottom: 10px
+  span.workflow_name
+    font-style: italic
+
+span.task_description
+  display: block
+  font-size: 1.5em
+  margin-bottom: 25px
+  border-bottom: solid 1px 
+
+form.task
+
+  label
+    display: block
+    &.radio_option
+      display: inline
+  textarea
+    width: 450px
+    height: 400px
+