rbbt-util 5.14.39 → 5.15.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: fb9eba165b567301078196458cb721d1ca1f130b
-  data.tar.gz: e2f067c01e6a2aff41d00d76d89fbad6c895678d
+  metadata.gz: a156a4d881f09ce0cbd2a74e878f682a294d2355
+  data.tar.gz: 5b85742823494158cbd422ae05eb49f1f9662cc1
 SHA512:
-  metadata.gz: e943920dabb8863f3fc5b1b142c7c02bd1ce1131ddf4173cf42463f4d77726bca36f700b50ba67aa0d6d952c3033f96f164009a626d3a2fd050cbd0db00201b7
-  data.tar.gz: 77591c927621415e7030ac7f8e4d2efad8d1c7b4b977c07147d49639de2ed1b8f018a753c32453830aa6e8a5585ad079730e3e56f86896d0859b159bc7a6ed48
+  metadata.gz: 5209b9ac5483a28bd744902435b3c194cad41814a7825b48302de178bbc84ed327069c266004db203befc403e3fb0ecebda6b4e96ea4dc3f5b580f64a8d8fb9e
+  data.tar.gz: e5ca07ed990db5ea1e4b4f5de902ea3c00e2d99960eb843b98306ea15550aa6e8e0e67893ba770bc0bcedc8b1b5e6f1e21829ea5e85595c935d18633edb633ee

data/etc/app.d/finder.rb

@@ -1,8 +1,9 @@
 #{{{ FINDER
 finder = Finder.new
 if ENV['RBBT_FINDER']
-  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => Organism.default_code("Hsa"), :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')})
-  finder.add_instance(Organism.lexicon(Organism.default_code("Hsa")), :persist => true, :namespace => Organism.default_code("Hsa"), :grep => '^LRG_', :invert_grep => true)
+  organism = Organism.default_code("Hsa")
+  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => organism, :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')}) if defined? KEGG
+  finder.add_instance(Organism.lexicon(organism), :persist => true, :namespace => organism, :grep => Organism.blacklist_genes(organism).list, :invert_grep => true) if defined? Organism
 end
 set :finder, finder
 Log.debug("Finder started with: #{finder.instances.length} instances")

data/share/rbbt_commands/workflow/server

@@ -13,10 +13,11 @@ require 'rbbt/rest/file_server'
 require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder"
 
 workflow = ARGV.first
 
+ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
 ENV["RServe-session"] = options[:RServe_session] || workflow
 
 raise rbbt_usage unless workflow
@@ -38,6 +39,10 @@ app.use Rack::Deflater
 
 load Rbbt.etc['app.d/resources.rb'].find
 
+app.class_eval do
+  eval Rbbt.etc['app.d/finder.rb'].read
+end
+
 WorkflowRest.add_workflow wf, true
 
 WorkflowRest.port = options[:port] || 4567

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.39
+  version: 5.15.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-11-20 00:00:00.000000000 Z
+date: 2014-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake