rbbt-util 5.17.61 → 5.17.62

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3b118eeecfa2079d442c02670893c6db20000987
-  data.tar.gz: 6263e5906f7b7749f5ceaef1cfae1937c2bd7348
+  metadata.gz: 0a158c34f2f9f67c5542d0b7807872a862bd78a8
+  data.tar.gz: 6e824cbc978e3de48ee2a1e67ae426e8a9b11a80
 SHA512:
-  metadata.gz: 10ac712ee0be37e90fd62ab1041fc58e198aa6eb90bf9563566a7e0c477f5dc9050303f0bcd7d49a1254ee1e3c4734686edf6c567a1c51c55814796059167ba7
-  data.tar.gz: edd7f314041feff12c71c178c2c1da63d9c776132df668cd74917beb129f51f7243fa2b6aba127c2a2ab3efe013d51020fc6bd69759cd54f36f475aa68f6b7c3
+  metadata.gz: b4dad4beb5c8e9ff8c859eec4c57c629752a98374ffba4fa6557698d762754155113d25aab8079b43e39c9fbbfd01123bc9ddd87cc9d5867c10d28c10ec0768a
+  data.tar.gz: 14c900e1dd0e09f6895b83faf4e8c605cd890caf8e7f4ef6088e85169b2b29f4e0f409aebe2dad2350ddcd42195b39b9b7a4ca9b10de39d5ea90779906b7ac56

data/etc/app.d/finder.rb

@@ -4,6 +4,12 @@ if ENV['RBBT_FINDER']
   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
+
+  mutation_hash = {"Genomic Mutation" => /\w+:\d+:[ACTG\-\+]+/}
+  finder.add_instance(mutation_hash, :namespace => organism) 
+
+  organism_hash = {"organism" => /[A-Z][a-z]{2}(?:\/[a-z]{3}20\d\d)?/}
+  finder.add_instance(organism_hash, :namespace => organism) 
 end
 set :finder, finder
 Log.debug("Finder started with: #{finder.instances.length} instances")

data/lib/rbbt/resource.rb

@@ -154,7 +154,7 @@ module Resource
                        content.call final_path
                      end
               case data
-              when String, IO
+              when String, IO, StringIO
                 Misc.sensiblewrite(final_path, data) 
               when Array
                 Misc.sensiblewrite(final_path, data * "\n")

data/lib/rbbt/rest/client/step.rb

@@ -153,7 +153,9 @@ class WorkflowRESTClient
 
     def recursive_clean
       begin
-        WorkflowRESTClient.get_raw(url, inputs.merge(:_update => :recursive_clean))
+        inputs = Array === self.inputs ? Hash[*self.inputs.flatten] : self.inputs
+        params = inputs.merge(:_update => :recursive_clean)
+        WorkflowRESTClient.get_raw(url, params)
       rescue Exception
         Log.exception $!
       end
@@ -162,7 +164,9 @@ class WorkflowRESTClient
 
     def clean
       begin
-        WorkflowRESTClient.get_raw(url, inputs.merge(:_update => :clean))
+        inputs = Array === self.inputs ? Hash[*self.inputs.flatten] : self.inputs
+        params = inputs.merge(:_update => :clean)
+        WorkflowRESTClient.get_raw(url, params)
       rescue Exception
         Log.exception $!
       end

data/lib/rbbt/util/misc/options.rb

@@ -69,7 +69,7 @@ module Misc
           when Array === v
             v * ","
           else
-            CGI.escape(v.to_s)
+            CGI.escape(v.to_s).gsub('%2F','/')
           end
       [ Symbol === k ? k.to_s : k,  v] * "="
     }.compact * "&"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.61
+  version: 5.17.62
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-14 00:00:00.000000000 Z
+date: 2015-07-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake