rbbt-rest 1.3.26 → 1.3.27

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 935dcbc86551da3d7d9365f6b8922cc976929542
+  metadata.gz: 03be0a1aa7c52a31f0138eecba03ebe8565f1b85
+  data.tar.gz: 80aeef50fc37891f40518f0e9d56654b846d2d24
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+  data.tar.gz: ec5b0e0eabf50b62ed9750fce4b5bce7eaa11f723e9286e06d997035edb8bb8bfffa6d527b2e724e31b0f7f8d6a8db894a50420bbe561f4dbcfa923dd201ae04

data/lib/rbbt/rest/knowledge_base.rb

@@ -11,6 +11,8 @@ module Sinatra
       base.module_eval do
         helpers KnowledgeBaseRESTHelpers
 
+        #{{{ Single entity
+        
         get '/knowledge_base/:name/:database/children/:entity' do 
           name = consume_parameter :name
           database = consume_parameter :database
@@ -110,6 +112,156 @@ module Sinatra
           end
         end
 
+        
+        #{{{ Collection
+
+        post '/knowledge_base/:name/:database/collection_children' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
+
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches = kb.children(database, entity)
+              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+            end
+            acc
+          }
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Children: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+             matches.each{|type,list|
+               _matches[type] = list.target
+             }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
+
+        post '/knowledge_base/:name/:database/collection_parents' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
+
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches = kb.parents(database, entity)
+              acc.merge!({ _matches.target_type => _matches}) if _matches and _matches.any?
+            end
+            acc
+          }
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+             matches.each{|type,list|
+               _matches[type] = list.target
+             }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
+
+        post '/knowledge_base/:name/:database/collection_neighbours' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          collection = consume_parameter :collection 
+          raise ParameterException, "No collection specified" if collection.nil?
+          collection = JSON.parse(collection)
+
+          kb = get_knowledge_base name
+          matches = collection.keys.inject({}){|acc,type|
+            entities = collection[type]
+            entities.each do |entity|
+              _matches_h = kb.neighbours(database, entity)
+              _matches_h.each do |key, _matches|
+                target_type = case key
+                              when :children
+                                _matches.target_type
+                              when :parents
+                                _matches.source_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?
+              end
+            end
+            acc
+          }
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Collection Parents: #{ [name, database] }")
+          when :json
+            content_type :json
+            _matches = {}
+             matches.each{|type,list|
+               _matches[type] = list.target
+             }
+            halt 200, _matches.to_json
+          else
+            content_type :text
+            matches = matches.sort_by{|k,list| list.length }.last.last
+            halt 200, matches.target * "\n"
+          end
+        end
+
+        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
+
         #{{{ Info
         
         get '/knowledge_base/info/:name/:database/:pair' do 

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

@@ -44,8 +44,12 @@ module KnowledgeBaseRESTHelpers
 
                                        kb.syndicate Genomics.knowledge_base, :genomics
 
+                                       TSV.traverse user_studies[user], :cpus => 10 do |study|
+                                         Study.setup(study)
+                                         study.sample_genes
+                                       end
+
                                        user_studies[user].each do |study|
-                                         next if study.all_mutations.length > 50_000
                                          kb.syndicate study.knowledge_base, study
                                        end
 

data/share/views/knowledge_base_partials/association.haml

@@ -1,22 +1,30 @@
 - values = index[pair] 
-- fields = index.fields
-- 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
 
 - source = pair.source_entity
 - target = pair.target_entity
 - source_name = source.respond_to?(:name) ? source.name || name : source
 - target_name = target.respond_to?(:name) ? target.name || name : target
 - name = [source_name, target_name] * "~"
-= tsv2html(tsv, :table_id => name)
+- kb_name = File.basename pair.knowledge_base.dir
+
+%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}

data/share/views/knowledge_base_partials/matches.haml

@@ -11,4 +11,5 @@
 - else
   = table do
     - matches = matches.values.sort{|v| v.length}.last if Hash === matches
+
     - matches.tsv

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.26
+  version: 1.3.27
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-18 00:00:00.000000000 Z
+date: 2014-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake