rbbt-study 0.2.8 → 0.2.9

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data/lib/rbbt/entity/study.rb

@@ -94,7 +94,7 @@ module Study
     if File.exists? setup_file
       base.instance_eval Open.read(setup_file), setup_file
     end
-    base.local_persist_dir = base.dir.var.cache.persistence.find
+    base.local_persist_dir = Rbbt.var.cache.studies[base].persistence.find
   end
 
   def self.studies

data/lib/rbbt/entity/study/genotypes/knowledge_base.rb

@@ -1,3 +1,8 @@
+require 'rbbt/workflow'
+Workflow.require_workflow "Genomics"
+require 'rbbt/entity/gene'
+require 'rbbt/entity/genomic_mutation'
+
 module Study
 
   self.study_registry[:mutation_genes] = Proc.new{|study,database|

data/lib/rbbt/entity/study/knowledge_base.rb

@@ -15,7 +15,7 @@ module Study
 
   def knowledge_base
     @knowledge_base ||= begin 
-                          kb = KnowledgeBase.new(self.dir.var.knowledge_base, self.organism)
+                          kb = KnowledgeBase.new(Rbbt.var.knowledge_base.studies[self], self.organism)
                           kb.format["Gene"] = "Ensembl Gene ID"
                           kb.entity_options["Sample"] = {"Study" => self}
                           Study.study_registry.each do |database, file|

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-study
 version: !ruby/object:Gem::Version
-  version: 0.2.8
+  version: 0.2.9
 platform: ruby
 authors:
 - Miguel Vazquez