rbbt-rest 1.1.4 → 1.1.5

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

@@ -20,6 +20,7 @@ module EntityRESTHelpers
     entity_annotations = {}
     entity_class.annotations.each do |annotation|
       value = consume_parameter annotation, params
+      value = Entity::REST.restore_element(value) if String === value
       value = false if value == "false"
       value = true if value == "true"
       entity_annotations[annotation] = value
@@ -71,6 +72,30 @@ module EntityRESTHelpers
 
     render(template_file, locals, layout_file, "Entity list #{ action }: #{ id }")
   end
+
+  def entity_map_render(map_id, type, column)
+    template_file = locate_entity_map_template(type, column)
+
+    map = Entity::Map.load_map(type, column, map_id, user)
+    locals = {:map => map, :map_id => map_id}
+
+    layout_file = layout ? locate_template("layout") : nil
+
+    render(template_file, locals, layout_file, "Entity map: #{ map_id }")
+  end
+
+  def entity_map_action_render(map, action, id, params = {})
+    template_file = locate_entity_map_action_template(map, action)
+
+    locals = params.merge({:map => map, :map_id => id})
+
+    layout_file = layout ? locate_template("layout") : nil
+
+    render(template_file, locals, layout_file, "Entity map #{ action }: #{ id }")
+  end
+
+
+
 end
 
 

data/lib/rbbt/rest/entity/rest.rb

@@ -14,15 +14,15 @@ module Entity
     #{{{ MISC
     
     def self.clean_element(elem)
-      elem.gsub('/', '--')
+      elem.gsub('/', '--').gsub('%', 'o-o')
     end
  
     def self.restore_element(elem)
-      CGI.unescape(elem.gsub('--', '/'))
+      CGI.unescape(CGI.unescape(elem.gsub('--', '/').gsub('o-o', '%')))
     end
 
     def entity_link_params
-      info = self.info
+      info = self.info.dup
       info.delete :format
       info.delete :annotation_types
       info.delete :annotated_array
@@ -65,7 +65,21 @@ module Entity
 
     #{{{ URLS
     
-    def self.entity_url(entity, type, params = {})
+    def self.entity_url(entity, type = nil, params = nil)
+      if type.nil?
+        type = entity.annotation_types.last.to_s
+        type << ":" << entity.format if entity.respond_to? :format
+      end
+
+      if params.nil?
+        if entity.respond_to? :entity_link_params
+          params = entity.entity_link_params
+        else
+          params = {}
+        end
+      end
+
+      params ||= entity.info if entity.respond_to? :info
       url = File.join('/', 'entity', Entity::REST.clean_element(type.to_s), entity) 
       url << "?" << Misc.hash2GET_params(params) if params.any?
       url
@@ -87,6 +101,20 @@ module Entity
       url
     end
 
+    def self.entity_map_url(map, type, column)
+      type = Entity::REST.clean_element(type.to_s)
+      column = Entity::REST.clean_element(column)
+      map = Entity::REST.clean_element(map)
+      File.join('/', 'entity_map', type,  column, map)
+    end
+
+    def self.entity_map_action_url(map, type, column, action)
+      type = Entity::REST.clean_element(type.to_s)
+      column = Entity::REST.clean_element(column)
+      map = Entity::REST.clean_element(map)
+      File.join('/', 'entity_map_action', type,  column, action, map)
+    end
+
 
     #{{{ LINKS
 
@@ -101,6 +129,7 @@ module Entity
 
       attributes[:class] << klasses
       attributes[:href] = Entity::REST.entity_url(self, entity_type.to_s, link_params)
+      attributes["attr-entity_id"] = self.to_s
 
       text = self.respond_to?(:name)? self.name || self : self if text.nil?
       attributes[:title] = text if attributes[:title].nil?

data/lib/rbbt/rest/main.rb

@@ -4,6 +4,7 @@ require 'rbbt/rest/common/users'
 require 'ruby-prof'
 
 require 'sinatra/base'
+require 'sinatra/cross_origin'
 require 'json'
 
 module Sinatra
@@ -21,18 +22,25 @@ module Sinatra
 
         set :cache_dir, Rbbt.var.sinatra.cache.find unless settings.respond_to? :cache_dir and settings.cache_dir != nil
         set :file_dir, Rbbt.var.sinatra.files.find unless settings.respond_to? :file_dir and settings.file_dir != nil
+        set :permalink_dir, Rbbt.var.sinatra.permalink.find unless settings.respond_to? :permalink_dir and settings.permalink_dir != nil
 
         set :public_folder, Rbbt.share.views.public.find 
 
         attr_accessor :ajax, :layout, :format, :size, :update, :cache_type, :_, :profile
 
-        set :haml, { :ugly => true }
         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
+        set :allow_methods, [:get, :post, :options]
+        set :allow_credentials, true
+        set :max_age, "1728000"
+        set :allow_headers, ['URI']
+
         before do
           Log.info("IP #{request.ip}: " << request.path_info << ". Params: " << Misc.remove_long_items(params).inspect)
           process_common_parameters
@@ -52,8 +60,7 @@ module Sinatra
             printer.print(:path => dir, :profile => 'profile')
             Log.info("Profile saved at #{ dir }")
           end
-
-          request
+          response.header["URI"] = request.env["REQUEST_URI"]
         end
 
         add_sass_load_path Rbbt.views.compass.find
@@ -92,9 +99,25 @@ module Sinatra
         end
 
         get '/' do
-          template_render('main', params)
+          template_render('main', params, 'main', :cache_type => :asynchronous)
         end
 
+        get '/help/?:section?' do
+          if params[:section]
+            section = params[:section]
+            template_render('help/' << section, params, section, :cache_type => :asynchronous)
+          else
+            template_render('help', params, 'help', :cache_type => :asynchronous)
+          end
+        end
+
+        get '/permalink/:id' do
+          content_type "text/html"
+          layout_file = locate_template('layout')
+          Haml::Engine.new(Open.read(layout_file), :filename => layout_file).render(self) do
+            Open.read(File.join(settings.permalink_dir, params[:id]))
+          end
+        end
       end
     end
   end

data/lib/rbbt/rest/workflow.rb

@@ -16,6 +16,7 @@ require 'json'
 
 module Sinatra
   module RbbtRESTWorkflow
+    WORKFLOWS = []
 
     def add_workflow_resource(workflow)
       views_dir = workflow.libdir.www.views.find(:lib)
@@ -32,12 +33,13 @@ module Sinatra
 
     def add_workflow(workflow, add_resource = false)
       raise "Provided workflow is not of type Workflow" unless  Workflow === workflow or WorkflowRESTClient === workflow
+      RbbtRESTWorkflow::WORKFLOWS.push workflow unless RbbtRESTWorkflow::WORKFLOWS.include? workflow
 
       add_workflow_resource(workflow) if add_resource
 
       Log.debug("Adding #{ workflow } to REST server")
 
-      self.instance_eval workflow.libdir.lib['sinatra.rb'].read if File.exists? workflow.libdir.lib['sinatra.rb']
+      self.instance_eval workflow.libdir.lib['sinatra.rb'].read, workflow.libdir.lib['sinatra.rb'].find if File.exists? workflow.libdir.lib['sinatra.rb']
 
       get "/#{workflow.to_s}" do
         case format
@@ -79,6 +81,10 @@ module Sinatra
         end
       end
 
+      get "/#{workflow.to_s}/description" do
+        halt 200, workflow.workflow_description
+      end
+
 
       get "/#{workflow.to_s}/:task" do
         task     = consume_parameter(:task)

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

@@ -90,9 +90,29 @@ module WorkflowRESTHelpers
   end
 
   def show_result(job, workflow, task)
-    case format
+    case format.to_sym
     when :html
       show_result_html job.load, workflow, task, job.name, job
+    when :table
+      halt 200, tsv2html(job.path, :url => "/" << [workflow.to_s, task, job.name] * "/")
+    when :entities
+      tsv = tsv_process(load_tsv(job.path).first)
+      list = tsv.values.flatten
+      if not AnnotatedArray === list and Annotated === list.first
+        list.first.annotate list 
+        list.extend AnnotatedArray
+      end
+      type = list.annotation_types.last
+      list_id = "TMP #{type} in #{ [workflow.to_s, task, job.name] * " - " }"
+      Entity::List.save_list(type.to_s, list_id, list, user)
+      redirect to(Entity::REST.entity_list_url(list_id, type))
+    when :map
+      tsv = tsv_process(load_tsv(job.path).first)
+      type = tsv.keys.annotation_types.last
+      column = tsv.fields.first
+      map_id = "MAP #{type}-#{column} in #{ [workflow.to_s, task, job.name] * " - " }"
+      Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
+      redirect to(Entity::REST.entity_map_url(map_id, type, column))
     when :json
       content_type "application/json"
       halt 200, job.load.to_json

data/share/views/compass/app.sass

@@ -1,4 +1,6 @@
 @import _foundation_setup
+@import style_mixins
+
 @import lists
 @import list_container
 @import dom
@@ -7,8 +9,6 @@
 @import tabs
 @import responsive_table
 
-@import style_mixins
-
 @import topbar
 @import favourites
 @import footer
@@ -17,6 +17,7 @@
 @import offcanvas
 @import fragment
 @import workflow
+@import reveal
 @import style
 
 body
@@ -26,13 +27,6 @@ body
 #body
   min-height: 900px
 
-
-//.main
-  dl
-    @extend dl.details
-    @extend .column
-    @extend .large-4
-
 ul.entities
   @extend .inline-list
   li
@@ -40,3 +34,17 @@ ul.entities
   
 dl.details
   @extend dl.indented
+
+
+.filter_controls
+  @media #{$medium} 
+    div.input
+      @include grid-column(4)
+      &.submit, &.submit > input
+        float: right
+        clear: both
+      label
+        @include ellipsis_text()
+
+.map_management ul
+  @include button-group-list()

data/share/views/compass/entity_card.sass

@@ -1,5 +1,5 @@
 // GRID LAYOUT
-.entity_card, .entity_list_card, .action_card
+.entity_card, .entity_list_card, .action_card, .entity_map_card
 
   & > .title
     @include grid-row(collapse)
@@ -49,9 +49,8 @@
     clear: left 
  
   
-.entity_card, .entity_list_card, .action_card
+.entity_card, .entity_list_card, .action_card, .entity_map_card
   & > .title
-    padding-top: 1em
     margin-bottom: 1em
 
     .name
@@ -98,3 +97,17 @@
         p
           text-align: justify
           max-width: 50em
+
+
+@media #{$not-small}
+  .reveal-modal
+    .entity_card, .entity_list_card, .action_card, .entity_map_card 
+      &> .card
+        &>.sidebar
+          width: 33% 
+        &>.content
+          width: 67%
+
+form.rename
+  input[name=rename]
+    width: 100%

data/share/views/compass/favourites.sass

@@ -1,5 +1,9 @@
-a#toggle_favourite
- 
+.reveal-modal a.toggle_favourite
+  &:not(.active)
+    i
+      color: black !important
+
+a#toggle_favourite, .reveal-modal a.toggle_favourite
   &.inactive
     span.remove
       display: none !important
@@ -26,6 +30,44 @@ a#toggle_favourite
         font-size: 0.5em
         margin-left: 1em
 
+ul.favourite_entity_lists
+  li
+    ul
+      li:not(.title)
+        +clearfix()
+        position: relative
+        width: 100%
+        padding-right: 3em
+        a 
+          min-height: 1em
+          display: inline-block !important
+          &.highlight
+            width: 3em !important
+            position: absolute
+            left: 0
+            &.active
+              i
+                color: yellow
+          &:not(.highlight)
+            position: relative
+            margin-left: 3em
+
+      
+ul.favourite_entities, ul.favourite_entity_lists, ul.favourite_entity_maps
+  ul.dropdown
+    li
+      @media #{ $not-small }
+        background: none repeat scroll 0 0 #00434C
+      a
+        @media #{ $not-small }
+          +ellipsis_text()
+          max-width: 400px
+        z-index: 9
+        &:not(.highlight):hover
+          white-space: normal !important
+          z-index: 10
+
+
 //@media only screen and (max-width: 767px) 
   #find_wrapper
     top: 9em

data/share/views/compass/form.sass

@@ -18,6 +18,13 @@
     margin-bottom: 2em
     label
       margin-bottom: 1em
+      &.inline
+        +ellipsis_text()
+        display: inline-block
+        clear: top
+        padding: 0
+        margin-bottom: 0
+        margin-left: 0.5em
 
   .input.submit
     clear: both
@@ -26,5 +33,9 @@
   select.favourite_lists
     width: 175px
 
+  span.choice
+    margin-right: 1em
+    white-space: nowrap
+
 .action_parameters form
   +clearfix()

data/share/views/compass/list_container.sass

@@ -24,7 +24,7 @@ dl.list_container
       a.entity_list
         display: block
         z-index: 15
-        margin-right: 1em
+        margin-right: 2em
         color: $primary-color
         width: 1.5em
         float: left

data/share/views/compass/reveal.sass

@@ -0,0 +1,31 @@
+.rbbt_reveal_content
+  display: none !important
+
+.reveal-modal a.toggle_favourite
+  &.active
+    i
+      color: #dd1 !important
+  &:not(.active)
+    i
+      color: black !important
+
+.reveal-modal .header
+  bottom-border: 1px solid grey
+  .close
+    float: right
+  .title
+    float: left
+
+.reveal-modal
+  .controls
+    a.link-reveal-modal
+      @include reveal-close()
+      right: 3em
+      font-size: 1em
+      top: 1.1em
+
+  &:not(.url)
+    .controls
+      a.link-reveal-modal
+        display: none
+