rbbt-rest 1.8.66 → 1.8.67

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c6df8d2c2bbdb1d5800f651260f183216749c0ca
-  data.tar.gz: f489484aa70c210f19b53d035106d737032e5e62
+  metadata.gz: 157083cd861ee7684a1f8aa8c6e467764926d330
+  data.tar.gz: 1d0e1ffebc9ff1a6800f639a92ae5340d50e3876
 SHA512:
-  metadata.gz: 25310a11efadbb3ff77c88467f5e98288e423044201dfc34bbd707aaef8971ed5146e487b861e371bd0ec19957741371757f00afd5680e540971d0e815ecbfda
-  data.tar.gz: afed826b530e611c5a844605ff3d686c2a3e4ec5498685e870f89a9fb30267659aeac164c0e20d316d3c4963568e36ea1b46fe66e6fe64a1411e1569ef1e3166
+  metadata.gz: aba24a6c098344fdae5db07e9ab514ced2c97edcfbcf710c30a3d5f534c21e5c3433f2c5d8b6e9fca770ad2d83bf34fa2bad9bb491645ac09b66df099c0b6dae
+  data.tar.gz: '0797a398dea30616971cf882ad50382ef827462346e869a3099213bb059f3148a545f9b79e987fb52c796e6f5878eaa39aabc1a74c73bfe6b7b4d0f5576898c5'

data/lib/rbbt/rest/graph.rb

@@ -0,0 +1,70 @@
+class RbbtGraph
+  attr_accessor :knowledge_base, :entities, :aesthetics, :associations, :rules
+
+  def initialize
+    @entities = {}
+    @aesthetics = {}
+    @associations = {}
+    @rules = {}
+  end
+
+  def add_associations(associations, type = :edge)
+    @associations[type] ||= []
+    @associations[type].concat associations.collect{|i| i }
+    @associations[type].uniq
+    if AssociationItem === associations
+      add_entities associations.target, associations.target_entity_type
+      add_entities associations.source, associations.source_entity_type
+    end
+  end
+
+  def add_entities(entities, type = nil, entity_options = {})                                                   
+    type = entities.base_entity.to_s if type.nil? and AnnotatedArray === entities
+    raise "No type specified and entities are not Annotated, so could not guess" if type.nil? 
+    if knowledge_base
+      good_entities = knowledge_base.translate(entities, type).compact.uniq
+    else
+      good_entities = entities
+    end
+    @namespace ||= entities.organism if entities.respond_to? :organism       
+    if @entities[type].nil?
+      @entities[type] = good_entities
+    else
+      @entities[type].concat good_entities
+    end
+  end                        
+
+  def add_aesthetic(elem, info)
+    @aesthetics[elem] ||= []
+    @aesthetics[elem] << info
+  end
+
+  def add_rule(elem, info)
+    @rules[elem] ||= []
+    @rules[elem] << info
+  end
+
+
+  def js_model
+    js_model = {:entities => {}, :associations => {}, :aes_rules => {}, :edge_aes_rules => {}, :rules => {}, :edge_rules => {}}
+    @entities.each do |type, codes|                                                                                          
+      info = codes.info if codes.respond_to? :info
+      info ||= {}
+      js_model[:entities][type] = {:codes => codes, :entity_type => type, :info => info}
+    end
+    @associations.each do |type, codes|
+      info = codes.info if codes.respond_to? :info
+      info ||= {}
+      js_model[:associations][type] = {:codes => codes, :database => type, :info => info}
+    end
+    @aesthetics.each do |type, info|
+      aes_rule_type = (type == :node ? :aes_rules : :edge_aes_rules)
+      js_model[aes_rule_type] = info
+    end
+    @rules.each do |type, info|
+      rule_type = (type == :node ? :rules : :edge_rules)
+      js_model[rule_type] = info
+    end
+    js_model
+  end
+end

data/share/views/layout/footer.haml

@@ -5,6 +5,10 @@
       opacity: 0.1
       filter: blur(3px) grayscale(100%)
 
+    .image
+      min-width: 50vm
+      a 
+        width: 100%
     .content
       display: block
     .header, .description

data/share/views/partials/dependencies.haml

@@ -5,10 +5,12 @@
     - dep_workflow ||= dep.task.workflow if dep.task
     - dep_workflow ||= File.basename(File.dirname(File.dirname(dep.path)))
     - str = [dep_workflow, dep.task_name, dep.name].compact * " - "
+    - dep_status = "done" if dep.path.exists?
+    - dep_status ||= dep.status
     - if dep.file(:progress).exists?
-      - status = dep.status.to_s + " - " + dep.file(:progress).yaml[:last_percent].to_s + "%"
+      - status = dep_status.to_s + " - " + dep.file(:progress).yaml[:last_percent].to_s + "%"
     - else
-      - status = dep.status
+      - status = dep_status
     - name = dep.name
     %li
       %span.workflow= dep_workflow
@@ -33,7 +35,7 @@
           = name 
 
 
-      %span.status(class="#{dep.status}") [#{status}]
+      %span.status(class="#{dep_status}") [#{status}]
 
       - if dep.dependencies.any?
         = partial_render('partials/dependencies', :job => dep)

data/share/views/partials/footers/bsc.haml

@@ -11,7 +11,7 @@
         font-weight: normal
         
     %span.bsc Barcelona Supercomputing Center
-    %span.cns Centro Nacional de Supercomputación
+    %span.cns Centro Nacional de Supercomputación
 
   .description
     %span.group Genome Informatics unit

data/share/views/public/js/rbbt.plots/rbbt.plots.aes.js

@@ -286,7 +286,6 @@ rbbt.plots.aes.set_aes = function(list, aes_rules, type){
     if (undefined === property && name == 'code') property = list.codes.slice()
     if (undefined === property) return
 
-    console.log([property, mapper, mapper_obj])
     var aes_values = rbbt.plots.aes.map_aesthetic(property, mapper, mapper_obj)
 
     if (undefined === list.aes[aes]){

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.66
+  version: 1.8.67
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-11 00:00:00.000000000 Z
+date: 2017-08-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -184,6 +184,7 @@ files:
 - lib/rbbt/rest/entity/render.rb
 - lib/rbbt/rest/entity/rest.rb
 - lib/rbbt/rest/file_server.rb
+- lib/rbbt/rest/graph.rb
 - lib/rbbt/rest/helpers.rb
 - lib/rbbt/rest/knowledge_base.rb
 - lib/rbbt/rest/knowledge_base/helpers.rb