rbbt-rest 1.4.3 → 1.4.4

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

@@ -0,0 +1,15 @@
+require 'rbbt/util/open'
+require 'rbbt/rest/common/render'
+
+require 'haml'
+module KnowledgeBaseRESTHelpers
+
+  def association_render(pair, database = nil)
+    database ||= pair.database
+    template_file = locate_association_template(database)
+
+    locals = {:pair => pair, :database => database}
+
+    render(template_file, locals, nil)
+  end
+end

data/lib/rbbt/rest/workflow.rb

@@ -11,6 +11,7 @@ require 'rbbt/rest/workflow/locate'
 require 'rbbt/rest/workflow/render'
 require 'rbbt/rest/workflow/jobs'
 
+
 require 'sinatra/base'
 require 'json'
 
@@ -22,6 +23,7 @@ module Sinatra
       views_dir = workflow.respond_to?(:libdir)? workflow.libdir.www.views.find(:lib) : nil
       if views_dir and views_dir.exists?
         Log.debug "Registering views for #{ workflow }: #{ views_dir.find }"
+        KnowledgeBaseRESTHelpers.association_resources.unshift views_dir
         EntityRESTHelpers.entity_resources.unshift views_dir
         RbbtRESTHelpers.template_resources.unshift views_dir
 

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

@@ -188,12 +188,10 @@ module WorkflowRESTHelpers
       end
 
       begin
-        job.fork 
-        job.grace
+        job.fork unless job.started?
 
         job_url = to(File.join("/", workflow.to_s, task, job.name)) 
         job_url += "?_format=#{@format}" if @format
-        #halt 200, job.name if format == :jobname
         if format == :jobname
           content_type :text
           job.name

data/share/views/association/Default.haml

@@ -0,0 +1,9 @@
+- database ||= pair.database
+
+- matrix = pair.knowledge_base.get_index(database).fields == ["Value"]
+
+- if matrix
+  = partial_render('knowledge_base_partials/association/value', :pair => pair, :knowledge_base => pair.knowledge_base, :database => database)
+- else
+  = partial_render('knowledge_base_partials/association/info', :pair => pair, :knowledge_base => pair.knowledge_base, :database => database)
+

data/share/views/compass/layout.sass

@@ -204,3 +204,18 @@ a.fragment
   width: 100%
   width: 2em
 
+@media #{$only-large}
+  .row
+    +clearfix()
+  .small_column
+    +span(1 of 3)
+    &:last-child
+      +span(last 1 of 3)
+    &:first-child
+      +span(first 1 of 3)
+  .column
+    +span(1 of 2)
+    &:last-child
+      +span(last 1 of 2)
+    &:first-child
+      +span(first 1 of 2)

data/share/views/compass/rbbt/table.sass

@@ -7,7 +7,9 @@ $color_table_border: darken($table_color, 45)
 
   caption
     text-align: left
-    margin-bottom: $vindent / 2
+    span
+      color: #999
+    //margin-bottom: $vindent / 2
 
   background-color: lighten($table_color, 5)
   border: 1px solid $color_table_border

data/share/views/entity_partials/list_container.haml

@@ -5,15 +5,21 @@
         - list = list.call
         - next if list.nil?
         %dt.next
-          = list.list_link :length, id
+          = list.respond_to?(:list_link) ? list.list_link(:length, id) : list.length
           %span.title
             = text || id 
         %dd
           - if (defined? force and force) or list.length < 500
-            = list.link * ", "
+            - if list.respond_to? :link
+              = list.link * ", "
+            - else
+              = list * ", "
           - else
             = modal_fragment "Too many entities to list" do
-              = list.link * ", "
+              - if list.respond_to? :link
+                = list.link * ", "
+              - else
+                = list * ", "
     - else
       - if list.empty?
         %dt
@@ -22,15 +28,21 @@
             = text || id 
       - else
         %dt.next
-          = list.list_link :length, id
+          = list.respond_to?(:list_link) ? list.list_link(:length, id) : list.length
           %span.title
             = text || id 
         %dd
           - if (defined? force and force) or list.length < 500
-            = list.link * ", "
+            - if list.respond_to? :link
+              = list.link * ", "
+            - else
+              = list * ", "
           - else
             = reveal "Too many entities to list" do
               = fragment do
-                = list.link * ", "
+                - if list.respond_to? :link
+                  = list.link * ", "
+                - else
+                  = list * ", "
 
 

data/share/views/knowledge_base_partials/association.haml

@@ -1,3 +1,4 @@
+- require 'rbbt/sources/PSI_MI'
 - values = index[pair] 
 
 - source = pair.source_entity
@@ -9,22 +10,24 @@
 
 %h3== #{name} in #{pair.database} #{kb_name}
 
-- fields = index.fields
-- if fields.any?
-  - tsv = TSV.setup({}, :key_field => "Num", :fields => fields, :type => :list)
-  - values.zip(fields).each_with_index do |p,i|
-    - value, field = p
-    - value.split(";;").each_with_index do |part,j|
-      - tsv[j] ||= [nil] * fields.length
-      - tsv[j][i] = part 
-  - tsv.entity_options = kb.entity_options
-  - tsv.namespace = kb.namespace
-
-  - if tsv.fields.include? "PMID"
-    - tsv.add_field "Title" do |k,v|
-      - v["PMID"].title
-
-  = tsv2html(tsv, :table_id => "#{pair} in #{pair.database} #{kb_name}")
-
-- else
-  No information for this association: #{pair}
+= association_render(pair, pair.database)
+
+
+- kb = pair.knowledge_base
+- other_databases = []
+
+- kb.registry.each do |database,info|
+  - index = kb.get_index database
+  - next unless index.include? pair
+  - next if database == pair.database
+  - other_databases << database
+
+- if other_databases.any?
+  %h5 In other databases
+
+
+  %dl.tabs
+    - other_databases.each do |database|
+      %dt.next=database
+      %dd
+        = association_render(pair, database)

data/share/views/knowledge_base_partials/association/info.haml

@@ -0,0 +1,38 @@
+- index = knowledge_base.get_index database
+
+- kb_name = File.basename pair.knowledge_base.dir
+
+- if index.include? pair
+  - fields = index.fields
+  - values = index[pair]
+
+  - if fields.any?
+    - tsv = TSV.setup({}, :key_field => "Num", :fields => fields, :type => :list)
+    - values.zip(fields).uniq.each_with_index do |p,i|
+      - value, field = p
+      - value.split(";;").each_with_index do |part,j|
+        - tsv[j] ||= [nil] * fields.length
+        - tsv[j][i] = part 
+    - tsv.entity_options = knowledge_base.entity_options
+    - tsv.namespace = knowledge_base.namespace
+
+    - if tsv.fields.include? "PMID"
+      - tsv.add_field "Title" do |k,v|
+        - v["PMID"].title
+
+    - if tsv.fields.include? "Publication"
+      - tsv.add_field "Title" do |k,v|
+        - PMID.setup(v["Publication"]).title if v["Publication"] =~ /^\d+$/
+
+    - if tsv.fields.include? "Method"
+      - tsv.add_field "Evidence" do |k,v|
+        - PSI_MITerm.setup(v["Method"]).name if v["Method"] =~ /^MI:\d+$/
+
+    -#= tsv2html(tsv, :table_id => "#{pair} in #{database} #{kb_name}")
+    = association_table tsv, :table_id => "#{pair} in #{database} #{kb_name}"
+
+  - else
+    No information for #{pair} in #{database}
+
+- else
+  Pair #{pair} not registered in #{ database }

data/share/views/knowledge_base_partials/association/value.haml

@@ -0,0 +1,13 @@
+- index = knowledge_base.get_index database
+- fields = index.fields
+
+- others = index.prefix(pair.source)
+
+- value = [index[pair]].flatten.first.to_f
+
+- rest = index.values_at(*others).flatten.compact.collect{|v| v and v =~ /\d/ ? v.to_f : nil}.compact
+
+%p= value
+
+= rest.sort * ", "
+

data/share/views/public/js/_ajax_replace.js

@@ -93,6 +93,7 @@ function replace_object(object, href, embedd, complete){
   if (embedd === undefined){ embedd = false; }
 
   object.addClass("embedded").attr('target-href', href)
+
   $.ajax({
     url : href,
     cache: false,
@@ -106,6 +107,7 @@ function replace_object(object, href, embedd, complete){
       error = $('<div>').append(error_span).append(error_message)
       object.removeClass("reloading").addClass("error").css('height', 0).html(error).css('height', 'auto').attr('target-href', href);
     },
+
     success: function( data, stat, req ) {
       object.removeClass('error');
       if (req.status == 202){
@@ -133,13 +135,13 @@ function replace_object(object, href, embedd, complete){
             href = remove_parameter(href, '_');
           }
           object.addClass("embedded").attr('target-href', href).get(0).innerHTML = data;
-            // eval js
           object.find('script').each(function(){eval(this.text = this.text || $(this).text())} );
 
           capture_embedded_form(object);
           update_rbbt();
         }else{
           object.replaceWith(data);
+
           update_rbbt();
         }
       }

data/share/views/public/js/rbbt/modal.js

@@ -3,60 +3,62 @@ $.widget("rbbt.modal", {
   },
 
   _reset_modal: function(modal_title, source_id){
-   var tool = this
-
-   var modal = this.element
-   modal.html('').addClass('modal')
-
-   var title = $('<div>').addClass('title')
-   if (modal_title !== undefined){ title.html(modal_title) }
-   var controls = $('<div>').addClass('controls')
-   controls.append($('<a>').addClass('toggle_favourite').append($('<i>').addClass('fi-star')))
-   controls.append($('<a>').addClass('link-reveal-modal').append($('<i>').addClass('fi-arrow-right')))
-   controls.append($('<a>').addClass('close-reveal-modal').append($('<i>').addClass('fi-x')))
-
-   var header = $('<div>').addClass('header').append(title).append(controls)
-
-   modal.append(header)
-   var content = $('<div>').addClass('content').html(content)
-   modal.attr('attr-reveal_source_id', source_id)
-   modal.on('click', 'a.close-reveal-modal', function(){ tool.close() })
-   modal.on('click', 'a.toggle_favourite', function(){ 
-    var url = $(tool.element).find('> .content').attr('target-href')
-    if (url !== undefined){
-     $('#top_menu li.favourites').favourites('toggle_page', url)
-    }
-    return false
-   })
+    var tool = this
+
+    var modal = this.element
+    modal.html('').addClass('modal')
+
+    var title = $('<div>').addClass('title')
+    if (modal_title !== undefined){ title.html(modal_title) }
+    var controls = $('<div>').addClass('controls')
+    controls.append($('<a>').addClass('toggle_favourite').append($('<i>').addClass('fi-star')))
+    controls.append($('<a>').addClass('link-reveal-modal').append($('<i>').addClass('fi-arrow-right')))
+    controls.append($('<a>').addClass('close-reveal-modal').append($('<i>').addClass('fi-x')))
+
+    var header = $('<div>').addClass('header').append(title).append(controls)
+
+    modal.append(header)
+    var content = $('<div>').addClass('content').html(content)
+    modal.attr('attr-reveal_source_id', source_id)
+    
+    modal.on('click', 'a.close-reveal-modal', function(){ tool.close() })
 
-   var content = $('<div>').addClass('content')
-   modal.append(content)
+    modal.on('click', 'a.toggle_favourite', function(){ 
+      var url = $(tool.element).find('> .content').attr('target-href')
+      if (url !== undefined){
+        $('#top_menu li.favourites').favourites('toggle_page', url)
+      }
+      return false
+    })
 
-   modal.removeClass('url').removeClass('entity')
+    var content = $('<div>').addClass('content')
+    modal.append(content)
 
-   return modal;
+    modal.removeClass('url').removeClass('entity')
+
+    return modal;
   },
 
   _shown_url: function(){
-   return $(this.element).find('> .content').attr('target-href')
+    return $(this.element).find('> .content').attr('target-href')
   },
 
   update_star: function(){
-   var url = this._shown_url()
-   if ($('#top_menu li.favourites').favourites('is_favourite', url)){
-    $(this.element).find('a.toggle_favourite').addClass('active');
-   }else{
-    $(this.element).find('a.toggle_favourite').removeClass('active');
-   }
+    var url = this._shown_url()
+    if ($('#top_menu li.favourites').favourites('is_favourite', url)){
+      $(this.element).find('a.toggle_favourite').addClass('active');
+    }else{
+      $(this.element).find('a.toggle_favourite').removeClass('active');
+    }
   },
 
   show: function(content, title, source_id){
-   var tool = this;
-   var modal = tool._reset_modal(title, source_id)
+    var tool = this;
+    var modal = tool._reset_modal(title, source_id)
 
-   modal.find('> .content').html(content)
-   this.element.show()
-   update_rbbt()
+    modal.find('> .content').html(content)
+    this.element.show()
+    update_rbbt()
   },
 
   ask: function(content, title, complete){
@@ -65,31 +67,32 @@ $.widget("rbbt.modal", {
   },
 
   show_url: function(url, title, source_id, complete){
-   var tool = this;
-   var modal = this._reset_modal(title, source_id)
+    var tool = this;
+    var modal = this._reset_modal(title, source_id)
+    tool.url = url
 
-   $('body').append(modal)
+    $('body').append(modal)
 
-   replace_object(modal.find('.content'), url, true, function(){
-    var url = tool._shown_url()
-    var url = remove_parameter(url, '_')
+    replace_object(modal.find('> .content'), url, true, function(){
+      var url  = tool.url 
+      url = remove_parameter(url, '_')
 
-    modal.addClass('url')
-    modal.find('.link-reveal-modal').attr('href', url)
+      modal.addClass('url')
+      modal.find('.link-reveal-modal').attr('href', url)
 
-    if (url != undefined && url.match(/^\/(?:entity|entity_list|entity_map)\//) != null){
-     modal.addClass('entity')
-     tool.update_star()
-    }
+      if (url != undefined && url.match(/^\/(?:entity|entity_list|entity_map)\//) != null){
+        modal.addClass('entity')
+        tool.update_star()
+      }
 
-    tool.element.show()
-    if (undefined !== complete){ complete()}
-    update_rbbt()
-   })
+      tool.element.show()
+      if (undefined !== complete){ complete()}
+      update_rbbt()
+    })
   },
 
   close: function(){
-   this.element.hide()
+    this.element.hide()
   }
 })
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.4.3
+  version: 1.4.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-19 00:00:00.000000000 Z
+date: 2014-09-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -204,7 +204,9 @@ files:
 - lib/rbbt/rest/helpers.rb
 - lib/rbbt/rest/knowledge_base.rb
 - lib/rbbt/rest/knowledge_base/helpers.rb
+- lib/rbbt/rest/knowledge_base/locate.rb
 - lib/rbbt/rest/knowledge_base/query.rb
+- lib/rbbt/rest/knowledge_base/render.rb
 - lib/rbbt/rest/main.rb
 - lib/rbbt/rest/monitor.rb
 - lib/rbbt/rest/web_tool.rb
@@ -212,6 +214,7 @@ files:
 - lib/rbbt/rest/workflow/jobs.rb
 - lib/rbbt/rest/workflow/locate.rb
 - lib/rbbt/rest/workflow/render.rb
+- share/views/association/Default.haml
 - share/views/compass/_rbbt.sass
 - share/views/compass/actions.sass
 - share/views/compass/app.sass
@@ -279,6 +282,8 @@ files:
 - share/views/job_result/tsv.haml
 - share/views/job_result/yaml.haml
 - share/views/knowledge_base_partials/association.haml
+- share/views/knowledge_base_partials/association/info.haml
+- share/views/knowledge_base_partials/association/value.haml
 - share/views/knowledge_base_partials/matches.haml
 - share/views/knowledge_base_partials/subset.haml
 - share/views/layout.haml