rbbt-util 5.25.4 → 5.25.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 53463985df5e51f4106125b28e2a26a052bc7ad1
-  data.tar.gz: 8215a6fdbebda4ad1b7b2277c05d5f041bd12e89
+  metadata.gz: e07b6ec4cc5c33daa9aa1ab26b968c7dd42b1c7d
+  data.tar.gz: 7a2cbbba275dac3f7981ce794468880faac8e306
 SHA512:
-  metadata.gz: dfcef6b4df76925ae979b43e50f851b8c288ed415aa76d1348670b06529df26485902388b2a0e2d3a06e67175001f3aa9f31c752db4112cb57c8b5f3b964ff17
-  data.tar.gz: 8c142f1a0eb354e0088e4c72ea917f5fe2237cf8a83d90a0177876e79ef10b90ad556d2a1f682b999888f78fc6bda207fc1db94f592d223077629039aaa6eb30
+  metadata.gz: 9a185e9f04e0be73b6d71b8d8358f4cd6c36669c7c93439e1e75876366a14b3aaf392f22be4fa0d19d363fd1256365d5e5258305e3fb9f3d1506aba862e7afc6
+  data.tar.gz: 02c0a3c7457da08b7445cfde0ef3e5799b69078a26a59b69f913b7c0f631647cf02e0cbb07ef821d82d193de0fd44a6a31dadda6ccbc3871e524183b78282fb3

data/lib/rbbt/knowledge_base/registry.rb

@@ -45,6 +45,9 @@ class KnowledgeBase
       begin 
         if options.empty?
           key = name.to_s
+        elsif options[:key]
+          key = options[:key]
+          key = name if key == :name
         else
           fp = Misc.hash2md5(options)
           key = name.to_s + "_" + fp
@@ -90,7 +93,13 @@ class KnowledgeBase
   def get_database(name, options = {})
     name = name.to_s
 
-    options[:organism] ||= options[:namespace] ||= self.namespace unless self.namespace.nil?
+    options = options.dup
+    if self.namespace == options[:namespace]
+      options.delete(:namespace) 
+    end
+    if self.namespace == options[:organism]
+      options.delete(:organism) 
+    end
     @databases[[name, options]] ||= 
       begin 
         fp = Misc.fingerprint([name,options])
@@ -102,6 +111,8 @@ class KnowledgeBase
           key = name.to_s + "_" + fp
         end
 
+        options[:organism] ||= options[:namespace] ||= self.namespace unless self.namespace.nil?
+
         key += '.database'
         Persist.memory("Database:" << [key, dir] * "@") do
           options = options.dup
@@ -124,14 +135,14 @@ class KnowledgeBase
           persist_options = Misc.pull_keys options, :persist
 
           database = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
-                    Log.low "Re-opening database #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
-                    Association.open(file, options, persist_options)
-                  else
-                    options = Misc.add_defaults options, registered_options if registered_options
-                    raise "Repo #{ name } not found and not registered" if file.nil?
-                    Log.medium "Opening database #{ name } from #{ Misc.fingerprint file }. #{options}"
-                    Association.open(file, options, persist_options)
-                  end
+                       Log.low "Re-opening database #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
+                       Association.open(file, options, persist_options)
+                     else
+                       options = Misc.add_defaults options, registered_options if registered_options
+                       raise "Repo #{ name } not found and not registered" if file.nil?
+                       Log.medium "Opening database #{ name } from #{ Misc.fingerprint file }. #{options}"
+                       Association.open(file, options, persist_options)
+                     end
 
           database.namespace = self.namespace if self.namespace
 

data/lib/rbbt/workflow/accessor.rb

@@ -640,6 +640,13 @@ class Step
     done? && info[:path] && info[:path] != path
   end
 
+  def knowledge_base(organism = nil)
+    @_kb ||= begin
+               kb_dir = self.file('knowledge_base')
+               KnowledgeBase.new kb_dir, organism
+             end
+  end
+
 end
 
 module Workflow

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.4
+  version: 5.25.5
 platform: ruby
 authors:
 - Miguel Vazquez