rbbt-rest 1.3.24 → 1.3.25

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 538af22c9217f13765f18be78f68df4bc21f89c0
-  data.tar.gz: f09cfbd38cd36048a974916d2bd048ad47914500
+  metadata.gz: ff57d6c10b5e72c5c364001762523ac37fd71bee
+  data.tar.gz: b2aa30882aa2b5f97dfc1302f6c2c73d92a9cf86
 SHA512:
-  metadata.gz: 9400cc1bac0e511d8047ef33c23f86f217d039ee0c170f149c65daabf28f2f61f076bcb3f54b972fb5509077a49c0063dc41c0eb07c9300efb5e6c059b6463de
-  data.tar.gz: f433926fff630aff9824f1e30c73fe07d4a1c084b8318876009897bd039933d64cc6c9e04122df56d2418febda1721b74e318691d46cda30fd8b8e067c25eb8f
+  metadata.gz: 7a747a879a08a4eb86bd2985f877344938b1ea8bb53ca02b4c51843436ae0fcb325ac7851191f415c6924aeb9e3ff58fee3d4084f7f207b81402e76ebf5f58a4
+  data.tar.gz: 9e0e7b4989f2542c7cef4ed99220857d3104f3ae4af3d1a4f6c0f61e258be60ae7afcb0dead43be946baabe266325cb52c159f14e553890d8951087f214a81d8

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

@@ -82,6 +82,8 @@ module RbbtRESTHelpers
       end
     end
 
+    @array_separator = consume_parameter(:_array_separator) || ','
+
     @permalink = consume_parameter :_permalink
 
     @clean_params = params.dup

data/lib/rbbt/rest/knowledge_base.rb

@@ -11,6 +11,105 @@ module Sinatra
       base.module_eval do
         helpers KnowledgeBaseRESTHelpers
 
+        get '/knowledge_base/:name/:database/children/:entity' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_knowledge_base name
+          matches = kb.children(database, entity)
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Children: #{ [name, database, entity] }")
+          when :json
+            content_type :json
+            halt 200, matches.target.to_json
+          else
+            content_type :text
+            halt 200, matches.target * "\n"
+          end
+        end
+
+        get '/knowledge_base/:name/:database/parents/:entity' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_knowledge_base name
+          matches = kb.parents(database, entity)
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            halt 200, matches.tsv.to_s
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => matches}, "Parents: #{ [name, database, entity] }")
+          when :json
+            content_type :json
+            halt 200, matches.source.to_json
+          else
+            content_type :text
+            halt 200, matches.source * "\n"
+          end
+        end
+
+        get '/knowledge_base/:name/:database/neighbours/:entity' do 
+          name = consume_parameter :name
+          database = consume_parameter :database
+          entity = consume_parameter :entity
+
+          kb = get_knowledge_base name
+          neighbours = kb.neighbours(database, entity)
+          case @format
+          when :tsv
+            content_type "text/tab-separated-values"
+            halt 200, neighbours.values.collect{|m| m.tsv.to_s } * "\n\n"
+          when :html
+            template_render('knowledge_base_partials/matches', {:matches => neighbours}, "Neighbours: #{ [name, database, entity] }")
+          when :json
+            content_type :json
+            neighs = {}
+            neighs[:parents] = neighbours[:parents].source if neighbours[:parents]
+            neighs[:children] = neighbours[:children].target
+            halt 200, neighs.to_json
+          else
+            content_type :text
+            neighs = []
+            neighs.concat neighbours[:parents].source if neighbours[:parents]
+            neighs.concat neighbours[:children].target
+            halt 200, neighs * "\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

@@ -56,7 +56,12 @@ module KnowledgeBaseRESTHelpers
   def get_knowledge_base(name, namespace = nil)
     @@knowledge_bases ||= IndiferentHash.setup({})
     @@knowledge_bases[name] ||= begin
-                                 kb = case 
+                                  begin
+                                    mod = Kernel.const_get name
+                                    return mod.knowledge_base if mod.respond_to? :knowledge_base
+                                  rescue Exception
+                                  end
+                                  kb = case 
                                       when [:genomics, "genomics"].include?(name)
                                         Genomics.knowledge_base
                                       when (Misc.path_relative_to(settings.cache_dir, name) and File.exists?(name))

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

@@ -40,6 +40,7 @@ module WorkflowRESTHelpers
 
   def execution_type(workflow, task)
     export = type_of_export(workflow, task)
+    return :sync if export == :exec and format == :html
     return export if export == :exec or cache_type.nil?
     return cache_type if cache_type
   end

data/share/views/knowledge_base_partials/matches.haml

@@ -0,0 +1,14 @@
+- if Hash === matches and matches.keys.length == 2 and matches.values.select{|v| v.any?}.length > 2
+  %h3 Parents
+  = table do
+    - matches = matches[:parents]
+    - matches.tsv
+
+  %h3 Children
+  = table do
+    - matches = matches[:children]
+    - matches.tsv
+- else
+  = table do
+    - matches = matches.values.sort{|v| v.length}.last if Hash === matches
+    - matches.tsv

data/share/views/knowledge_base_partials/subset.haml

@@ -0,0 +1,7 @@
+= table do
+  - fields = subset.info_fields
+  - type = [subset.source_type, subset.target_type] * "~"
+  - tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => subset.namespace)
+  - subset.each do |match|
+    - tsv[match] = match.info.values_at *fields
+  - tsv

data/share/views/public/js/helpers.js

@@ -59,7 +59,6 @@ function parse_parameters(params){
 function require_js(url, success){
   var async = false;
   var cache = production;
-  console.log("Require js: " + url)
   if (undefined === success){
     async = false;
   }else{
@@ -68,9 +67,6 @@ function require_js(url, success){
 
   url = url.replace('/js/', '/js-find/')
   $.ajax({url: url, cache:cache, dataType:'script', async: async, success: success} ).fail(function(jqxhr, settings, exception){
-    console.log('Exception loading: ' + url)
-    console.log(exception)
-    console.log(jqxhr)
   })
 }
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.24
+  version: 1.3.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-15 00:00:00.000000000 Z
+date: 2014-07-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -277,6 +277,8 @@ 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/matches.haml
+- share/views/knowledge_base_partials/subset.haml
 - share/views/layout.haml
 - share/views/layout/top_menu.haml
 - share/views/layout/top_menu/favourites.haml