rbbt-rest 1.6.28 → 1.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7cc64722779414103b76baf41c3b2d7e8f0508b2
-  data.tar.gz: 3b787d34032bc0744a2425c179b4603fe30470c6
+  metadata.gz: c26433848653c8f1bd15c43ca516eed2e6d9eaa9
+  data.tar.gz: a92d6b2af8de46ba913ad5cbf8d04da099ff2df1
 SHA512:
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-  data.tar.gz: 412f73b81453ec5c8725b9e784b23eada13ef3f74941a31f0d7146bfddcd1bc390d446291c12dc619eb2059300f2e297362128aea8a5013061c1caa647e80a36
+  metadata.gz: df25f492e6e7e206899526ffe96b5afcdeb9b96b1dcc119ca491be465c5bb3d512c7beed852171ee8bc4035d2c083d80da8f5fa4d9710d6cb18ea5026ab65c0a
+  data.tar.gz: dcc46801b37da11055bc42e55212884b169f590e90848f7e203e43b5efc6f848554fd6dec6b68008b9fd28633e605930d811180317096240d35f95b1f0fb9b3d

data/lib/rbbt/rest/entity.rb

@@ -75,7 +75,7 @@ module Sinatra
 
           @entity = entity
 
-          entity_render(entity)
+          entity_render(entity, @clean_params)
         end
 
         get '/entity_action/:entity_type/:action/:entity' do
@@ -429,6 +429,76 @@ module Sinatra
           redirect to(Entity::REST.entity_map_url(new_id, entity_type, column))
         end
 
+        #{{{{{{{{{{{{{{
+        #{{{ PROPERTIES
+        #{{{{{{{{{{{{{{
+
+        get '/entity_property/:property/:entity_type/:entity' do
+          entity_type = consume_parameter :entity_type
+          entity = consume_parameter :entity
+          property = consume_parameter :property
+          args = consume_parameter :args
+
+          if args.nil?
+            args = []  
+          else
+            args = begin
+                     JSON.parse(args)
+                   rescue
+                     args
+                   end
+          end
+
+          case args
+          when Hash
+            args = [args] 
+          when String
+            args = args.split(/[,\|]/)
+          end
+
+          entity_type = Entity::REST.restore_element(entity_type)
+
+          entity = setup_entity(entity_type, entity, @clean_params)
+
+          content_type "application/json"
+          halt 200, entity.send(property,*args).to_json
+        end
+
+        get '/entity_list_property/:property/:entity_type/:list_id' do
+          entity_type = consume_parameter :entity_type
+          list_id = consume_parameter :list_id
+          property = consume_parameter :property
+
+          args = consume_parameter :args
+
+          if args.nil?
+            args = []  
+          else
+            args = begin
+                     JSON.parse(args)
+                   rescue
+                     args
+                   end
+          end
+
+          case args
+          when Hash
+            args = [args] 
+          when String
+            args = args.split(/[,\|]/)
+          end
+
+
+          entity_type = Entity::REST.restore_element(entity_type)
+          list_id = Entity::REST.restore_element(list_id)
+
+          list = Entity::List.load_list(entity_type.split(":").first, list_id, user)
+
+          content_type "application/json"
+          halt 200, list.send(property, *args).to_json
+        end
+
+
         #{{{{{{{{{{{{{{
         #{{{ FAVOURITES
         #{{{{{{{{{{{{{{

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

@@ -33,10 +33,11 @@ module EntityRESTHelpers
     entity
   end
 
-  def entity_render(entity)
+  def entity_render(entity, params = {})
     template_file = locate_entity_template(entity)
 
-    locals = {:entity => entity}
+    params = {} if params.nil?
+    locals = {:entity => entity}.merge(params)
 
     layout_file = layout ? locate_template("layout") : nil
 

data/lib/rbbt/rest/knowledge_base.rb

@@ -87,14 +87,44 @@ module Sinatra
           end
         end
 
-        get '/knowledge_base/:name/:database/subset' do 
+        #get '/knowledge_base/:name/:database/subset' do 
+        #  name = consume_parameter :name
+        #  database = consume_parameter :database
+        #  source = consume_parameter :source
+        #  target = consume_parameter :target
+
+        #  source = source == "all" ? :all : source.split(@array_separator) if source
+        #  target = target == "all" ? :all : target.split(@array_separator) if target
+        #  entities = { :source => source, :target => target }
+
+        #  kb = get_knowledge_base name
+        #  subset = kb.subset(database, entities)
+        #  case @format
+        #  when :tsv
+        #    content_type "text/tab-separated-values"
+        #    halt 200, subset.tsv.to_s
+        #  when :html
+        #    template_render('knowledge_base_partials/subset', {:subset => subset}, "Subset: #{ [name, database] }")
+        #  when :json
+        #    content_type :json
+        #    halt 200, subset.source.to_json
+        #  else
+        #    content_type :text
+        #    halt 200, subset.source * "\n"
+        #  end
+        #end
+
+        route :get, :post, '/knowledge_base/:name/:database/subset' do 
           name = consume_parameter :name
           database = consume_parameter :database
           source = consume_parameter :source
           target = consume_parameter :target
 
+          target = source if target.nil?
+
           source = source == "all" ? :all : source.split(@array_separator) if source
           target = target == "all" ? :all : target.split(@array_separator) if target
+
           entities = { :source => source, :target => target }
 
           kb = get_knowledge_base name
@@ -103,6 +133,9 @@ module Sinatra
           when :tsv
             content_type "text/tab-separated-values"
             halt 200, subset.tsv.to_s
+          when :tsv_json
+            content_type :json
+            halt 200, subset.tsv.to_json
           when :html
             template_render('knowledge_base_partials/subset', {:subset => subset}, "Subset: #{ [name, database] }")
           when :json
@@ -129,7 +162,14 @@ module Sinatra
             entities = collection[type]
             entities.each do |entity|
               _matches = kb.children(database, entity)
-              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+              type = _matches.target_type
+              next unless _matches and _matches.any?
+              if (acc[type])
+                acc[type].concat(_matches)
+              else
+                acc[type] = _matches
+              end
+              acc
             end
             acc
           }
@@ -138,6 +178,11 @@ module Sinatra
             content_type "text/tab-separated-values"
             matches = matches.sort_by{|k,list| list.length }.last.last
             halt 200, matches.tsv.to_s
+          when :tsv_json
+            content_type :json
+            halt 200, {}.to_json if matches.empty?
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_json
           when :html
             template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Children: #{ [name, database] }")
           when :json
@@ -166,7 +211,14 @@ module Sinatra
             entities = collection[type]
             entities.each do |entity|
               _matches = kb.parents(database, entity)
-              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+              type = _matches.target_type
+              next unless _matches and _matches.any?
+              if acc[type]
+                acc[type].concat(_matches)
+              else
+                acc[type] = _matches
+              end
+              acc
             end
             acc
           }
@@ -175,6 +227,11 @@ module Sinatra
             content_type "text/tab-separated-values"
             matches = matches.sort_by{|k,list| list.length }.last.last
             halt 200, matches.tsv.to_s
+          when :tsv_json
+            content_type :json
+            halt 200, {}.to_json if matches.empty?
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_json
           when :html
             template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
           when :json
@@ -236,34 +293,32 @@ module Sinatra
           end
         end
 
-        get '/knowledge_base/:name/:database/subset' do 
+        #{{{ Info
+
+        get '/knowledge_base/:name/:database/info' do 
           name = consume_parameter :name
           database = consume_parameter :database
-          source = consume_parameter :source
-          target = consume_parameter :target
-
-          source = source == "all" ? :all : source.split(@array_separator) if source
-          target = target == "all" ? :all : target.split(@array_separator) if target
-          entities = { :source => source, :target => target }
 
           kb = get_knowledge_base name
-          subset = kb.subset(database, entities)
-          case @format
-          when :tsv
-            content_type "text/tab-separated-values"
-            halt 200, subset.tsv.to_s
-          when :html
-            template_render('knowledge_base_partials/subset', {:subset => subset}, "Subset: #{ [name, database] }")
-          when :json
-            content_type :json
-            halt 200, subset.source.to_json
-          else
-            content_type :text
-            halt 200, subset.source * "\n"
-          end
-        end
 
-        #{{{ Info
+          source = kb.source(database)
+          target = kb.target(database)
+          source_type = kb.source_type(database)
+          target_type = kb.target_type(database)
+          source_entity_options = kb.entity_options_for source_type
+          target_entity_options = kb.entity_options_for target_type
+
+          info = {
+            :source => source,
+            :target => target,
+            :source_type => source_type,
+            :target_type => target_type,
+            :source_entity_options => source_entity_options,
+            :target_entity_options => target_entity_options,
+          }
+
+          halt 200, info.to_json
+        end
 
         get '/knowledge_base/info/:name/:database/:pair' do 
           name = consume_parameter :name
@@ -459,7 +514,6 @@ module Sinatra
           found = kb.identify database, entity
           raise ParameterException, "Entity #{entity} was not found" unless found
 
-          iii kb.children(database, found)
           list = kb.children(database, found).target_entity
 
           content_type "application/json"
@@ -475,7 +529,6 @@ module Sinatra
           found = kb.identify database, entity
           raise ParameterException, "Entity #{entity} was not found" unless found
 
-          iii kb.parents(database, found)
           list = kb.parents(database, found).target_entity
 
           content_type "application/json"

data/lib/rbbt/rest/main.rb

@@ -6,6 +6,7 @@ require 'ruby-prof'
 
 require 'sinatra/base'
 require 'sinatra/cross_origin'
+require "sinatra/multi_route"
 require 'json'
 
 module Sinatra
@@ -36,6 +37,8 @@ module Sinatra
 
     def self.registered(base)
       base.module_eval do
+        register Sinatra::MultiRoute
+
         helpers RbbtRESTHelpers
         register Sinatra::RbbtAuth
 

data/lib/rbbt/rest/workflow.rb

@@ -143,7 +143,7 @@ module Sinatra
           error = job.error? || job.aborted?
 
           if done
-            show_result job, workflow, task
+            show_result job, workflow, task, params
           else
             if started
               exec_type = execution_type(workflow, task) 

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

@@ -58,10 +58,11 @@ module WorkflowRESTHelpers
     task_inputs
   end
 
-  def show_result_html(result, workflow, task, jobname = nil, job = nil)
+  def show_result_html(result, workflow, task, jobname = nil, job = nil, params = nil)
+    params ||= {}
     result_type = workflow.task_info(task)[:result_type]
     result_description = workflow.task_info(task)[:result_description]
-    workflow_render('job_result', workflow, task, :result => result, :type => result_type, :description => result_description, :jobname => jobname, :job => job)
+    workflow_render('job_result', workflow, task, {:result => result, :type => result_type, :description => result_description, :jobname => jobname, :job => job}.merge(params))
   end
 
   def show_exec_result(result, workflow, task)
@@ -92,12 +93,12 @@ module WorkflowRESTHelpers
     end
   end
 
-  def show_result(job, workflow, task)
+  def show_result(job, workflow, task, params = nil)
     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
+      show_result_html job.load, workflow, task, job.name, job, params
     when :table
       halt 200, tsv2html(job.path, :url => "/" << [workflow.to_s, task, job.name] * "/")
     when :entities

data/share/views/compass/app.sass

@@ -18,6 +18,7 @@ $subtle-font: rgba(0,0,0,0.30)
 
 body
   background: none repeat scroll 0% 0% #F7F7F7
+  font-family: Helvetica
 
 #content
   padding: 0px 48px 0 48px
@@ -99,7 +100,11 @@ body
   .action_content
     clear: both
   
-  
+.action_controller > .action_menu 
+  width: calc(100% - 48px)
+  & > .button 
+    max-width: 25%
+
 .entity_card, .entity_list_card, .action_card
   > .content > .ui.basic.segment, > .action_content > .ui.basic.segment
     padding: 0px
@@ -146,14 +151,17 @@ body
     width: 10em
     display: inline-block
 
-.figure.float
-  float: left
-  margin-right: 32px
-  background: white
-  border: 1px solid rgba(0,0,0,0.12)
-  padding: 4px
+.figure
+  margin-bottom: 1em
+  margin-top: 1em
   .title
     color: $subtle-font
+  &.float
+    float: left
+    margin-right: 32px
+    background: white
+    border: 1px solid rgba(0,0,0,0.12)
+    padding: 4px
 
 .tool_menu
   margin-bottom: 0px
@@ -227,10 +235,6 @@ a.entity.highlight
   @extend .bulleted
   font-weight: bold
 
-.figure
-  margin-bottom: 1em
-  margin-top: 1em
-
 
 a.entity[data-aes-color]:not([data-aes-color=none])
   @extend .bulleted
@@ -412,3 +416,9 @@ body
 
 .list_comparison > li > a
   margin-left: 1em
+
+td
+  &.true
+    color: green
+  &.false
+    color: red

data/share/views/layout/footer.haml

@@ -6,7 +6,6 @@
     .ui.header
       CNIO. Centro Nacional de Investigaciones Oncologicas (Spanish National Cancer Research Center)
     .description
-      %br/
       %span.group Structural Computational Biology Group
       %br/
       %span.address   C/ Melchor Fernandez Almagro, 3, E-28029 Madrid

data/share/views/layout/header.haml

@@ -10,6 +10,7 @@
 
 
 - record_css '/plugins/semantic-ui/dist/semantic.min.css'
+- record_css '/plugins/nvd3/css/nv.d3.css'
 -# record_css '/plugins/jquery-ui/css/custom-theme/jquery-ui-1.8.14.custom.css'
 - record_css '/stylesheets/app'
 = serve_css
@@ -21,14 +22,11 @@
   var main_url = window.location.toString();
   var production = #{production? ? "true" : "false"};
 
--#= link_js "http://cdnjs.cloudflare.com/ajax/libs/mithril/0.1.28/mithril.min.js"
-
 - record_js '/js/defer'
 - record_js "/plugins/mithril/js/mithril.js"
-- record_js "/plugins/requirejs/js/require.js"
+-# record_js "/plugins/requirejs/js/require.js"
 = serve_js
-
-:javascript
+-#:javascript
   requirejs.config({baseUrl: '/js-find'})
 
 
@@ -41,6 +39,11 @@
 - record_js '/plugins/semantic-ui/dist/semantic.min.js'
 - record_js '/plugins/FileSaver/js/FileSaver.js'
 - record_js '/plugins/color-js/color.js'
+- record_js '/plugins/d3js/js/d3js.min.js'
+- record_js '/plugins/nvd3/js/nv.d3.js'
+- record_js '/plugins/svg-pan-zoom/js/svg-pan-zoom.js'
+- record_js '/plugins/cola/js/cola.v3.min.js'
+- record_js '/plugins/mithril-node-render/js/index.js'
 
 - %w(helpers _md5 _ajax_replace _ellipsis).each do |file|
   - record_js "/js-find/#{ file }"
@@ -49,7 +52,7 @@
 - %w(dom_update fragment actions table list map reveal).each do |file|
   - record_js "/js-find/rbbt/#{ file }"
 
-- %w(rbbt rbbt.basic rbbt.exception rbbt.job rbbt.page rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.knowledge_base rbbt.aesthetics rbbt.modal).each do |file|
+- %w(rbbt rbbt.basic rbbt.exception rbbt.job rbbt.page rbbt.entity rbbt.entity_list rbbt.entity_map rbbt.views rbbt.favourites rbbt.knowledge_base rbbt.aesthetics rbbt.plots rbbt.modal).each do |file|
   - record_js "/js-find/#{ file }"
 
 - record_js "/js-find/app"