rbbt-rest 1.4.10 → 1.4.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7238b912c301e0c3359e037b1c067332a8f6b413
-  data.tar.gz: 502e447f4643efa03d48f63d22cc356e8c320623
+  metadata.gz: 79c5f4dab3cb27a5c2a52674a04fb02bf8257417
+  data.tar.gz: eb2d80aa0d553528c8556d56a47df3fbffabd185
 SHA512:
-  metadata.gz: 5bc4bfcecac880d3855f412135959b0a4b4ae66e24e6f5368be23c00a5f6a21d33c76d95f38842a9f9b0b5dd8b28a60e6b7fec09d9536c1aa9b8ed293cfbe37c
-  data.tar.gz: d9ed1bf96e0e8c7c9c52ff30b9921b1512cdc6dad883aa6ce5d57dcf4772b483600e8ffabd69975438bd51ebd7676e02fc65b63c1c9770358394c6c4c4092caa
+  metadata.gz: 25e607bce141f788bb50288933599d26f7563c6812df719e9d161624c1c5fb1cb1a7417010af2209a27b83e536017210749816480bb769c87a99cc595279f742
+  data.tar.gz: 6105e96305d4e1b71068ef30874576e41f2f04d73f5797bd826dec2940600cb84845e98d7d1a7132533d7d597b1e681d87eeb5f544057ed94ea20184a54e2d63

data/lib/rbbt/rest/client/step.rb

@@ -26,7 +26,7 @@ class WorkflowRESTClient
       (Array === @url ? @url.first : @url).split("/")[-2]
     end
 
-    def info
+    def info(check_lock=false)
       @info ||= begin
                   init_job unless url
                   info = WorkflowRESTClient.get_json(File.join(url, 'info'))

data/lib/rbbt/rest/common/cache.rb

@@ -28,7 +28,7 @@ module RbbtRESTHelpers
     orig_name = name
     name += "_" << Misc.hash2md5(params) if params.any?
 
-    path = settings.cache_dir[name].find
+    path = params[:cache_file] || settings.cache_dir[name].find
     task = Task.setup(:name => orig_name, :result_type => :string, &block)
 
     step = Step.new(path, task, nil, nil, self)
@@ -128,6 +128,7 @@ module RbbtRESTHelpers
         step.run 
       else
         step.fork
+        step.soft_grace
       end
     end
 

data/lib/rbbt/rest/common/forms.rb

@@ -16,7 +16,7 @@ module RbbtRESTHelpers
   end
 
   def file_or_text_area(id, name, value, tsv = false)
-    text_area_string = tsv ? "or use the text area bellow (you may use ',' intead of tabs)" : "or use the text area bellow"
+    text_area_string = tsv ? "or use the text area below (you may use ',' intead of tabs)" : "or use the text area below"
 
     html_tag("input", nil, :type => "file", :id => (id.nil? ? nil : id +  "__" + "param_file"), :name => name.to_s + "__" + "param_file") + 
     html_tag("span", text_area_string, :class => "file_or_text_area") + 
@@ -75,8 +75,8 @@ module RbbtRESTHelpers
       end
 
       input_label(id, name, description, default, extra) +
-        html_tag("input", nil, :type => :hidden, :name => name.to_s + "_checkbox_false", :value => "false") +
-        html_tag("input", nil, :type => :checkbox, :checked => check_true, :name => name, :value => "true", :id => id)
+        html_tag("input", nil, :type => :checkbox, :checked => check_true, :name => name, :value => "true", :id => id) +
+        html_tag("input", nil, :type => :hidden, :name => name.to_s + "_checkbox_false", :value => "false") 
 
     when :string, :float, :integer, :hidden
       value = current.nil?  ? default : current
@@ -94,7 +94,7 @@ module RbbtRESTHelpers
              when :string
                nil
              when :float
-               "any"
+               "0.1"
              when :integer
                1
              end
@@ -107,10 +107,10 @@ module RbbtRESTHelpers
       value = value * "\n" if Array === value
 
       if no_file
-        input_label(id, name, description, default, extra) +
+        input_label(id, name, description, nil, extra) +
           html_tag("textarea", value || "" , :name => name, :id => id )
       else
-        input_label(id, name, description, default, extra) +
+        input_label(id, name, description, nil, extra) +
           file_or_text_area(id, name, value, type == :tsv)
       end
 

data/lib/rbbt/rest/common/locate.rb

@@ -10,7 +10,7 @@ module RbbtRESTHelpers
   end
 
   def template_resources
-   [Rbbt.www.views.find(:lib)] + RbbtRESTHelpers.template_resources
+   [Rbbt.www.views] + RbbtRESTHelpers.template_resources
   end
   
   def locate_template_from_resource(resource, template)
@@ -26,6 +26,29 @@ module RbbtRESTHelpers
     raise TemplateMissing, "Template #{ template } not found"
   end
  
+  #{{{ TEMPLATE
+  
+  def self.file_resources
+    @file_resources ||= template_resources
+  end
+
+  def file_resources
+   [Rbbt.www.views] + RbbtRESTHelpers.file_resources
+  end
+  
+  def locate_file_from_resource(resource, file)
+    resource[file]
+  end   
+
+  def locate_file(file)
+    file_resources.each do |resource|
+      path = locate_file_from_resource(resource, file)
+      return path if path.exists?
+    end
+
+    raise TemplateMissing, "File #{ file } not found"
+  end
+
   #{{{ SASS
   
   def self.add_sass_load_path(path)
@@ -37,7 +60,7 @@ module RbbtRESTHelpers
   end
 
   def sass_resources
-    RbbtRESTHelpers.sass_resources
+    [Rbbt.www.views.compass] + RbbtRESTHelpers.sass_resources
   end
 
   def locate_sass_from_resource(resource, template)

data/lib/rbbt/rest/common/misc.rb

@@ -221,16 +221,32 @@ module RbbtRESTHelpers
 end
 
 require 'haml'
-module Haml::Filters::DefferJS
+module Haml::Filters::DeferJS
   include Haml::Filters::Base
 
   def render(text)
-    deffer_text =<<-EOF
-:javascript
-  deffer(function(){
-#{text.gsub(/^/,"    ")}
-  })
+    defer_text =<<-EOF
+%script(defer)
+  :plain
+    defer(function(){
+#{text.gsub(/^/,"      ")}
+    })
 EOF
-    Haml::Engine.new(deffer_text).to_html  # gfm method defined elsewhere
+    Haml::Engine.new(defer_text).to_html 
+  end
+end
+
+require 'haml'
+module Haml::Filters::Documentation
+  include Haml::Filters::Base
+
+  def render(text)
+    doc_text =<<-EOF
+%section.documentation#{ text.gsub(/\s/,'').length < 80 * 10 ? '.short' : ''}
+  :markdown
+#{text.gsub(/^/,"    ")}
+    EOF
+
+    Haml::Engine.new(doc_text).to_html  
   end
 end

data/lib/rbbt/rest/common/render.rb

@@ -34,6 +34,7 @@ module RbbtRESTHelpers
 
   def wait_on(job, layout = nil)
     3.times do
+      raise RbbtRESTHelpers::Retry if job.done? or job.error?
       sleep 1
     end
 
@@ -54,18 +55,15 @@ module RbbtRESTHelpers
     layout_file = layout_file.find if layout_file.respond_to? :find
     template_file = template_file.find if layout_file.respond_to? :find
     if layout_file
-      #Haml::Engine.new(Open.read(layout_file), :filename => layout_file, :ugly => production?).render(self, locals) do
       Tilt::HamlTemplate.new(layout_file, :filename => layout_file, :ugly => production?).render(self, locals) do
         cache(cache, locals.merge(:_template_file => template_file, :user => user).merge(cache_options)) do
           Log.debug{ "Rendering #{template_file} with layout" }
-          #Haml::Engine.new(Open.read(template_file), :filename => template_file, :ugly => production?).render(self, locals)
           Tilt::HamlTemplate.new(template_file, :filename => template_file, :ugly => production?).render(self, locals)
         end
       end
     else
       cache(cache, locals.merge(:_template_file => template_file, :user => user).merge(cache_options)) do
         Log.debug{ "Rendering #{template_file} without layout" }
-        #Haml::Engine.new(Open.read(template_file), :filename => template_file, :ugly => production?).render(self, locals)
         Tilt::HamlTemplate.new(template_file, :filename => template_file, :ugly => production?).render(self, locals)
       end
     end

data/lib/rbbt/rest/common/table.rb

@@ -29,6 +29,50 @@ module Link
   end
 end
 
+module Change
+  extend Entity
+
+  self.format =(<<-EOF
+Change
+                EOF
+               ).split("\n")
+
+  def <=>(other)
+    self.scan(/\d+/).first.to_f <=> other.scan(/\d+/).first.to_f
+  end
+
+  def self.tsv_sort(v)
+    value = v.last
+    if Array === value
+      value.first.scan(/\d+/).first.to_f
+    else
+      value.scan(/\d+/).first.to_f
+    end
+  end
+end
+
+module Location
+  extend Entity
+
+  self.format =(<<-EOF
+Location
+                EOF
+               ).split("\n")
+
+  def <=>(other)
+    self.to_s.split(":").first.to_f <=> other.to_s.split(":").first.to_f
+  end
+
+  def self.tsv_sort(v)
+    value = v.last
+    if Array === value
+      value.first.to_s.split(":").first.to_f
+    else
+      value.to_s.split(":").first.to_f
+    end
+  end
+end
+
 module NumericValue
   extend Entity
 
@@ -51,6 +95,10 @@ adjusted.p.value
 adjusted.p.values
 Rank
 rank
+Counts
+Ratio
+Size
+size
                 EOF
                ).split("\n")
 
@@ -128,7 +176,7 @@ module RbbtRESTHelpers
 
     num = num.to_i
     size = size.to_i
-    max = object.size / size + 1
+    max = (object.size / size) + 1
 
     num = max if num > max
     num = - max if num < - max
@@ -178,7 +226,7 @@ module RbbtRESTHelpers
         
         case
         when value =~ /^([<>]=?)(.*)/
-          tsv = tsv.select(key, invert){|k| k = k.first if Array === k; (k.nil? or k.empty?) ? false : k.to_f.send($1, $2.to_f)}
+          tsv = tsv.select(key, invert){|k| k = k.first if Array === k; (k.nil? or (String === k and k.empty?)) ? false : k.to_f.send($1, $2.to_f)}
         when value =~ /^\/(.+)\/.{0,2}\s*$/
           tsv = tsv.select({key => Regexp.new($1)}, invert)
         when (value =~ /^\d+$/ and tsv.type == :double or tsv.type == :flat)
@@ -286,7 +334,8 @@ module RbbtRESTHelpers
       url = remove_GET_param(url, "_")
     end
 
-    table_class = []
+    table_class = options[:table_class] || []
+    table_class = [table_class] unless Array === table_class
     table_class << 'wide responsive' if tsv.fields.length > 4
 
     options[:url] = url

data/lib/rbbt/rest/main.rb

@@ -31,11 +31,6 @@ module Sinatra
 
         attr_accessor :ajax, :layout, :format, :size, :update, :cache_type, :_, :profile
 
-        if production?
-          set :haml, { :ugly => true }
-          set :clean_trace, true
-          set :static_cache_control , [:public, {:max_age => 360000}]
-        end
 
         enable :cross_origin
         set :allow_origin, :any
@@ -44,9 +39,18 @@ module Sinatra
         set :max_age, "1728000"
         set :allow_headers, ['URI']
 
+        if production?
+          set :haml, { :ugly => true }
+          set :clean_trace, true
+          set :static_cache_control , [:public, {:max_age => 360000}]
+        else
+          set :static_cache_control , [:public, {:max_age => 0}]
+        end
+
         before do
           method = request.request_method
           method_color = case method
+
           when "GET"
             :cyan
           when "POST"
@@ -179,6 +183,18 @@ module Sinatra
 
           halt 500, [e.class.to_s, e.message] * " => " << "\n\n" << (e.backtrace * "\n").gsub('`',"'")
         end
+
+        get '/fonts/*' do
+          filename = params[:splat].first
+          file = File.join(FontAwesome::Sass.fonts_path, filename)
+          send_file file
+        end
+
+        get '/opt/*' do
+          filename = params[:splat].first
+          file = locate_file(Path.setup('public/opt')[filename])
+          send_file file.find
+        end
         
         require 'rbbt/rest/monitor'
         register Sinatra::RbbtRESTMonitor

data/lib/rbbt/rest/web_tool.rb

@@ -2,6 +2,7 @@
 module Sinatra
   module RbbtToolHelper
     def tool(toolname, options = {})
+      options[:id] ||= toolname.to_s + "_#{rand(10000)}"
       partial_render("tools/#{toolname}", options)
     end
   end

data/lib/rbbt/rest/workflow.rb

@@ -217,7 +217,26 @@ module Sinatra
 
         job = workflow.load_id(File.join(task, job))
 
-        send_file job.file(filename)
+        require 'mimemagic'
+        path = job.file(filename)
+        mime = nil
+        Open.open(path) do |io|
+          begin
+            mime = MimeMagic.by_path(io) 
+            if mime.nil?
+              io.rewind
+              mime = MimeMagic.by_magic(io) 
+            end
+            if mime.nil?
+              io.rewind
+              mime = "text/tab-separated-values" if io.gets =~ /^#/ and io.gets.include? "\t"
+            end
+          rescue Exception
+            Log.exception $!
+          end
+        end
+        content_type mime if mime
+        send_file path
       end
 
       delete "/#{workflow.to_s}/:task/:job" do

data/lib/rbbt/rest/workflow/jobs.rb

@@ -98,6 +98,8 @@ module WorkflowRESTHelpers
   end
 
   def show_result(job, workflow, task)
+    return show_result_html nil, workflow, task, job.name, job if @fragment
+
     case format.to_sym
     when :html
       show_result_html job.load, workflow, task, job.name, job
@@ -196,7 +198,7 @@ module WorkflowRESTHelpers
           content_type :text
           job.name
         else
-          job.grace
+          job.soft_grace
           redirect job_url
         end
       rescue Exception

data/lib/rbbt/rest/workflow/render.rb

@@ -6,6 +6,7 @@ module WorkflowRESTHelpers
   def workflow_render(template, workflow = nil, task = nil, params = {})
     workflow = consume_parameter(:workflow, params) if workflow.nil?
     task     = consume_parameter(:task, params) if workflow.nil?
+    job      = consume_parameter(:job, params) if job.nil?
 
     template_file = locate_workflow_template(template, workflow, task)
 
@@ -13,9 +14,22 @@ module WorkflowRESTHelpers
     locals[:workflow] = workflow if workflow
     locals[:task]     = task if task
 
-    layout_file = layout ? locate_template("layout") : nil
-
-    render(template_file, locals, layout_file)
+    if layout
+      layout_file = workflow.libdir.www.views[workflow.to_s]["layout.haml"] if workflow.libdir
+      layout_file = locate_template("layout") unless layout_file and layout_file.exists?
+    else
+      layout_file = nil
+    end
+
+    if job 
+      locals[:job]      = job 
+      @step = job
+      cache_type = execution_type(workflow, task)
+      cache_file = job.file('html')
+      render(template_file, locals, layout_file, [task,workflow,job.name] * "-", :cache_type => cache_type, :cache_file => cache_file)
+    else
+      render(template_file, locals, layout_file)
+    end
   end
 
   def workflow_partial(template, workflow = nil, task = nil, params = {})

data/share/views/compass/_app.sass

@@ -0,0 +1,17 @@
+@import "_normalize"
+@import "_rbbt"
+
+@import "style"
+
+@import "user"
+@import "entity_card"
+@import "workflow"
+@import "finder"
+@import "favourites"
+@import "actions"
+@import "top_menu"
+@import "help"
+@import "figure"
+@import "monitor"
+@import "layout"
+