rbbt-rest 1.3.31 → 1.3.32

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 0208f7fc3e2046cb4ddd0124670584543dddf184
-  data.tar.gz: feb9543f611a596b3dc4ffef0d0148b7184640aa
+  metadata.gz: baafff671bbb97e58be46dfcaaee6a3c64b103b4
+  data.tar.gz: d7106534d2b1b70944e2bc875b7cbeadef8c26a6
 SHA512:
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-  data.tar.gz: 0e7ebfce95a3c73df346d73e3969c885c1ec6bff560a2c6c5d676945788adc0526cf2778f7426bd58b9d87fb89cc4524b12adbe74ae0218e833fd79a3ba837be
+  metadata.gz: 098f9a74ed00d545f866e0d397a131191c2d14c8078ba09156a7694d253320ebae52268a80808969410cd05b694725af8a08e45bc665b3569876ea19806d5a0a
+  data.tar.gz: d36a5bc597de18f4214be7d0179030e3354080c6b6834132cecd0ed2e2314c4701c8f4650082da8c0ac30a5ca7a3f8157e4ccfc157db9c60d8652c639d6dfb5d

data/lib/rbbt/rest/client.rb

@@ -26,13 +26,20 @@ class WorkflowRESTClient
   def job(task, name, inputs)
     task_info = task_info(task)
     fixed_inputs = {}
+    input_types = task_info[:input_types]
+
     inputs.each do |k,v| 
-      fixed_inputs[k] = case v
-                        when TSV
-                          v.to_s
-                        else
-                          v
-                        end
+      k = k.to_sym
+      if TSV === v
+        fixed_inputs[k] = v.to_s
+      else
+        case input_types[k].to_sym
+        when :tsv, :array, :file, :text
+          fixed_inputs[k] = (String === v and Open.exists?(v)) ? Open.open(v) : v
+        else
+          fixed_inputs[k] = v
+        end
+      end
     end
 
     RemoteStep.new(url, task, name, fixed_inputs, task_info[:result_type], task_info[:result_description], @exec_exports.include?(task))

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

@@ -118,11 +118,20 @@ module RbbtRESTHelpers
     when :boolean
       param2boolean(value)
 
-    when :text
+    when :text, :file
       if param_file and (value.nil? or (String === value and value.empty?))
         param_file[:tempfile].read
       else
-        value.gsub(/\r\n/, "\n")
+        case value
+        when String
+          value.gsub(/\r\n/, "\n")
+        when File, IO
+          value
+        when Hash
+          value[:tempfile]
+        else
+          raise "Missing class for #{ type }: #{ Misc.fingerprint value }"
+        end
       end
 
     when :array

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

@@ -75,11 +75,11 @@ module Entity
         if entity.respond_to? :entity_link_params
           params = entity.entity_link_params
         else
-          params = {}
+          params = entity.respond_to?(:info) ? entity.info : {}
         end
       end
 
-      params ||= entity.info if entity.respond_to? :info
+
       url = File.join('/', 'entity', Entity::REST.clean_element(type.to_s), entity) 
       url << "?" << Misc.hash2GET_params(params) if params.any?
       url

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

@@ -3,10 +3,19 @@ require 'rbbt/knowledge_base'
 
 module KnowledgeBaseRESTHelpers
   class << self
-    attr_accessor :knowledge_base_dir, :knowledge_bases
+    attr_accessor :knowledge_base_dir, :syndications
+
+    def add_syndication(name, kb)
+      @syndications ||= {}
+      @syndications[name] = kb
+    end
+
+    def syndications
+      @syndications ||= {}
+    end
   end
 
-  self.knowledge_base_dir     = "var/knowledge_base"
+  self.knowledge_base_dir     = Path.setup("var/sinatra/knowledge_bases")
 
   def prepare_entities_for_json(entities)
     case entities
@@ -25,65 +34,90 @@ module KnowledgeBaseRESTHelpers
     end
   end
 
-  def get_kb(name)
-    @@knowledge_bases ||= IndiferentHash.setup({})
-    case name
-    when :genomics, "genomics"
-      @@knowledge_bases[name] ||= Genomics.knowledge_base
-    else
-      @@knowledge_bases[name] ||= KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
-    end
-  end
+  #def get_kb(name)
+  #  @@knowledge_bases ||= IndiferentHash.setup({})
+  #  case name
+  #  when :genomics, "genomics"
+  #    @@knowledge_bases[name] ||= Genomics.knowledge_base
+  #  else
+  #    @@knowledge_bases[name] ||= KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
+  #  end
+  #end
+
+  #def user_kb(user)
+  #  user = "guest" if user.nil?
+  #  @@user_knowledge_bases ||= IndiferentHash.setup({})
+  #  @@user_knowledge_bases[user] ||= begin
+  #                                     kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), Organism.default_code("Hsa")
+  #                                     kb.format["Gene"] = "Ensembl Gene ID"
+
+  #                                     kb.syndicate Genomics.knowledge_base, :genomics
+
+  #                                     if defined? user_studies
+  #                                       TSV.traverse user_studies[user], :cpus => 10 do |study|
+  #                                         Study.setup(study)
+  #                                         study.sample_genes if study.has_genotypes?
+  #                                       end 
+
+  #                                       user_studies[user].each do |study|
+  #                                         Study.setup(study)
+  #                                         kb.syndicate study.knowledge_base, study
+  #                                       end
+  #                                     end
+
+  #                                     kb
+  #                                   end
+  #end
+
+  #def get_knowledge_base(name, namespace = nil)
+  #  @@knowledge_bases ||= IndiferentHash.setup({})
+  #  @@knowledge_bases[name] ||= begin
+  #                                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))
+  #                                      KnowledgeBase.new name
+  #                                    when KnowledgeBase.registry.include?(name)
+  #                                      KnowledgeBase.registry[name]
+  #                                    when (defined? Study and Study.studies.include?(name))
+  #                                      Study.setup(name).knowledge_base
+  #                                    when name.to_s == "user"
+  #                                      user_kb(user)
+  #                                    else
+  #                                      KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
+  #                                    end
+
+  #                               namespace ? kb.version(namespace) : kb
+  #                             end
+  #end
 
   def user_kb(user)
-    user = "guest" if user.nil?
-    @@user_knowledge_bases ||= IndiferentHash.setup({})
-    @@user_knowledge_bases[user] ||= begin
-                                       kb = KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, File.join('user', user)), Organism.default_code("Hsa")
-                                       kb.format["Gene"] = "Ensembl Gene ID"
-
-                                       kb.syndicate Genomics.knowledge_base, :genomics
-
-                                       if defined? user_studies
-                                         TSV.traverse user_studies[user], :cpus => 10 do |study|
-                                           Study.setup(study)
-                                           study.sample_genes if study.has_genotypes?
-                                         end 
-
-                                         user_studies[user].each do |study|
-                                           Study.setup(study)
-                                           kb.syndicate study.knowledge_base, study
-                                         end
-                                       end
-
-                                       kb
-                                     end
+    @@user_kbs ||= {}
+    @@user_kbs[user] ||= begin
+                           kb = KnowledgeBase.new(KnowledgeBaseRESTHelpers.knowledge_base_dir.users[user], Organism.default_code("Hsa"))
+                           
+                           KnowledgeBaseRESTHelpers.syndications.each do |name, new|
+                             Log.low "Syndicating database #{ name } for user #{user}"
+                             kb.syndicate name, new
+                           end if KnowledgeBaseRESTHelpers.syndications.any?
+
+                           kb
+                         end
   end
 
-  def get_knowledge_base(name, namespace = nil)
-    @@knowledge_bases ||= IndiferentHash.setup({})
-    @@knowledge_bases[name] ||= begin
-                                  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))
-                                        KnowledgeBase.new name
-                                      when KnowledgeBase.registry.include?(name)
-                                        KnowledgeBase.registry[name]
-                                      when (defined? Study and Study.studies.include?(name))
-                                        Study.setup(name).knowledge_base
-                                      when name.to_s == "user"
-                                        user_kb(user)
-                                      else
-                                        KnowledgeBase.new File.join(KnowledgeBaseRESTHelpers.knowledge_base_dir, name)
-                                      end
-
-                                 namespace ? kb.version(namespace) : kb
-                               end
+  def get_knowledge_base(name=:user, namespace = nil)
+    kb = case name.to_s
+           when "user"
+             user_kb(user)
+           else
+             Genomics.knowledge_base
+           end
+
+    (namespace and namespace != kb.namespace) ? kb.version(namespace) : kb
   end
 end

data/lib/rbbt/rest/knowledge_base.rb

@@ -270,7 +270,7 @@ module Sinatra
           database = consume_parameter :database
           pair = consume_parameter :pair
 
-          kb = get_knowledge_base name
+          kb = get_knowledge_base 
           index = kb.get_index(database)
 
           AssociationItem.setup(pair, kb, database, false)

data/lib/rbbt/rest/workflow.rb

@@ -100,7 +100,7 @@ module Sinatra
       end
 
       get "/#{workflow.to_s}/description" do
-        halt 200, workflow.workflow_description
+        halt 200, workflow.documentation[:description] || ""
       end
 
 

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

@@ -3,6 +3,8 @@ $margin_table_actions: 7px
 $padding_table: 5px 7px
 $color_table_border: darken($table_color, 45)
 =rbbt_table()
+  min-width: 300px
+
   caption
     text-align: left
     margin-bottom: $vindent / 2

data/share/views/compass/style.sass

@@ -1,2 +1,3 @@
 .menu_item
   +_rbbt_menu_item
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.3.31
+  version: 1.3.32
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-28 00:00:00.000000000 Z
+date: 2014-08-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake