rbbt-rest 1.3.27 → 1.3.28

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 03be0a1aa7c52a31f0138eecba03ebe8565f1b85
-  data.tar.gz: 80aeef50fc37891f40518f0e9d56654b846d2d24
+  metadata.gz: 3ee101d0492e48680b0abec1e9087e59695bc35f
+  data.tar.gz: b5d1de6388c52f93f677197a936b2e2fb9e12493
 SHA512:
-  metadata.gz: 5a7faedf99cebb0e4e173f74bdf2974794d81afe55f3806a20bff814595192380150b9f9038a3ad69870c1bab19fdbebcb5f45f47cd25364efe4dd1251365dc9
-  data.tar.gz: ec5b0e0eabf50b62ed9750fce4b5bce7eaa11f723e9286e06d997035edb8bb8bfffa6d527b2e724e31b0f7f8d6a8db894a50420bbe561f4dbcfa923dd201ae04
+  metadata.gz: 1a032336cd44ebaa2f8f7bdfba3529739c1197d0a624cdf7d6a65322fd916342dc3f1e3c800b690d1a111b2b36f9651a1dbdbe29314b1bb92f7a0a41a0adfe1c
+  data.tar.gz: dcb22d712b035d08ba9862fbdc7eb47a2b1c20e626d0d322ef381313bdd0a7cec81247a15f01f75b2d784b2f05d21dd81cd4b06dd39e4580989b129829a2d0f4

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

@@ -5,14 +5,16 @@ module Link
 
   def self.tsv_sort(v)
     value = v.last
-    value = value.first if Array === value
-    if value and value.match(/<a [^>]*>([^>]*)<\/a>/)
+    value = value.first if Array === value and value.length == 1
+    if String === value and value.match(/<a [^>]*>([^>]*)<\/a>/)
       val = $1
       if val =~ /^\s*\d/
         val.to_f
       else
-        val
+        1
       end
+    elsif Array === value
+      value.length
     else
       0
     end

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

@@ -56,11 +56,11 @@ module EntityRESTHelpers
 
   def find_all_entity_action_templates_from_resource(resource, entity)
     if entity == "Default" 
-      resource.entity["Default"].glob("*.haml")
+      resource.entity["Default"].glob("*.haml").sort
     else
       entity.annotation_types.collect do |annotation|
         resource.entity[annotation].glob('*.haml')
-      end.compact.flatten
+      end.compact.flatten.sort
     end
   end   
 
@@ -192,11 +192,11 @@ module EntityRESTHelpers
   def find_all_entity_list_action_templates_from_resource(resource, entity)
 
     if entity == "Default" 
-      resource.entity_list["Default"].glob("*.haml")
+      resource.entity_list["Default"].glob("*.haml").sort
     else
       entity.annotation_types.collect do |annotation|
         resource.entity_list[annotation].glob('*.haml')
-      end.compact.flatten
+      end.compact.flatten.sort
     end
   end   
 

data/lib/rbbt/rest/knowledge_base.rb

@@ -204,16 +204,17 @@ module Sinatra
               _matches_h.each do |key, _matches|
                 target_type = case key
                               when :children
-                                _matches.target_type
+                                _matches.target_entity_type
                               when :parents
-                                _matches.source_type
+                                _matches.source_entity_type
                               end
                 _matches = acc[target_type].concat _matches if acc[target_type] and acc[target_type].any?
-                acc.merge!({ target_type => _matches}) if _matches and _matches.any?
+                acc.merge!({ target_type => _matches }) if _matches and _matches.any?
               end
             end
             acc
           }
+
           case @format
           when :tsv
             content_type "text/tab-separated-values"
@@ -225,7 +226,7 @@ module Sinatra
             content_type :json
             _matches = {}
              matches.each{|type,list|
-               _matches[type] = list.target
+               _matches[type] = list.target.uniq.sort
              }
             halt 200, _matches.to_json
           else

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

@@ -46,10 +46,11 @@ module KnowledgeBaseRESTHelpers
 
                                        TSV.traverse user_studies[user], :cpus => 10 do |study|
                                          Study.setup(study)
-                                         study.sample_genes
-                                       end
+                                         study.sample_genes if study.has_genotypes?
+                                       end 
 
                                        user_studies[user].each do |study|
+                                         Study.setup(study)
                                          kb.syndicate study.knowledge_base, study
                                        end
 

data/share/views/entity_partials/action_controller.haml

@@ -7,9 +7,9 @@
         %a.reload_action(href="#" title="Refresh action")
           %i.general.fi-refresh
 
-      %li.url
-        %a(href="#" title="Bookmark action")
-          %i.general.fi-bookmark
+      %li.description
+        %a(href="#" title="View description")
+          %i.general.fi-book
 
       %li.parameters
         %a(href="#" title="Configure parameters")
@@ -19,14 +19,14 @@
         %a(href="#" title="Make this configuration default")
           %i.general.fi-paperclip
 
-      %li.description
-        %a(href="#" title="View description")
-          %i.general.fi-book
+      %li.url
+        %a(href="#" title="Bookmark action")
+          %i.general.fi-bookmark
 
 
     %ul.actions
       - last_resource = nil
-      - controller.actions.reverse.each do |action, text, resource, params|
+      - controller.actions.each do |action, text, resource, params|
         %li(class="#{last_resource and last_resource != resource ? "new_resource" : ""}" attr-resource="#{resource}")
           - case
           - when AnnotatedArray === entity

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.27
+  version: 1.3.28
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-02 00:00:00.000000000 Z
+date: 2014-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake