rbbt-util 5.17.31 → 5.17.32

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ec2769ac8dcfb78a8e3b33cdf905f2b0e53e9340
-  data.tar.gz: 9362e1f40b97de7451f0f4ed7467a7f386745128
+  metadata.gz: c98abc284aedb4105b8168c0860250a1acc2f3f8
+  data.tar.gz: 868baa16f1fe6f287f9b6ad793d14608fb0b49cb
 SHA512:
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-  data.tar.gz: 53fdcaded28ebccbe7f88335e3448046300698554deba0bcf3e44b478ea131229128c2b2460f8db18e0ad3f67d83c425020c89bb22013c707a2c377a281937f2
+  metadata.gz: 23c3a24f663d611f2fa838b86c2231433b0c52cac8d8d7a3f4e4665f46b5421436e05a6c27b90fb3f16534dfd4efcf9280ba6f79104ec154ef155087824b3964
+  data.tar.gz: 2001725c848637abccf349964c8bcf16751849afb85898d6b67b90ed07b5878b19b1724a33d9ee4e41937946305557045b4bba0833a2d6a7db54e2825bf24c46

data/bin/rbbt

@@ -75,6 +75,7 @@ if mem_dump = options.delete(:dump_mem)
   Rbbt.dump_memory(mem_dump, Symbol)
 end
 
+
 if options.delete :nostream
   ENV["RBBT_NO_STREAM"] = "true"
 end

data/lib/rbbt/knowledge_base/syndicate.rb

@@ -1,7 +1,11 @@
 class KnowledgeBase
   def syndicate(name, kb)
     kb.all_databases.each do |database|
-      db_name = [database, name] * "@"
+      if name.nil?
+        db_name = database
+      else
+        db_name = [database, name] * "@"
+      end
       file, kb_options = kb.registry[database]
       options = {}
       options[:entity_options] = kb_options[:entity_options]

data/lib/rbbt/tsv/change_id.rb

@@ -111,6 +111,7 @@ module TSV
             return index
           end
         rescue Exception
+          Log.exception $!
           Log.error "Exception reading identifier file: #{file.find}"
         end
       end

data/lib/rbbt/tsv/manipulate.rb

@@ -21,6 +21,14 @@ module TSV
       [key, new]
     end
 
+    def process_reorder_single(key, values)
+      new_key = @new_key_field == :key ? key : values
+      new_value = @new_fields.collect{|field| field == :key ?  key : values }.first
+      return [new_key, new_value]
+      [ [values[@new_key_field]], 
+        @new_fields.collect{|field| field == :key ?  key : values[field] }]
+    end
+
     def process_reorder_list(key, values)
       [ [values[@new_key_field]], 
         @new_fields.collect{|field| field == :key ?  key : values[field] }]
@@ -141,6 +149,8 @@ module TSV
           end
         when :flat
           self.instance_eval do alias process process_reorder_flat end
+        when :single
+          self.instance_eval do alias process process_reorder_single end
         else
           self.instance_eval do alias process process_reorder_list end
         end
@@ -561,7 +571,6 @@ module TSV
     field_pos = identify_field field
 
     through do |key, values|
-
       case
       when type == :single
         field_values = values

data/lib/rbbt/util/R/eval.rb

@@ -83,6 +83,7 @@ module R
 
                            bin_path = File.join(ENV["R_HOME"], "bin/Rserve")
                            cmd = bin_path + " " + args*" "
+                           $stdout.reopen File.new('/dev/null', 'w')
                            exec(ENV, cmd)
                          end
                          while not File.exists? pid_file

data/share/rbbt_commands/app/template

@@ -13,7 +13,7 @@ require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 require 'rbbt/rest/web_tool'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*:-w--workflows*"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*"
 
 template = ARGV.first
 

data/share/rbbt_commands/workflow/task

@@ -187,6 +187,8 @@ the job dependencies recursively.
 --load_inputs* Load inputs from a directory
 --info Show the job info:
 --provenance Report the jobs provenance:
+-W--workflows* Load a list of workflows
+-R--requires* Require a list of files
 EOF
 
 workflow = ARGV.shift
@@ -216,6 +218,22 @@ end
 
 workflow = Workflow.require_workflow workflow
 
+if options[:workflows]
+  require 'rbbt/workflow'
+  workflows = options[:workflows].split(',')
+  workflows.each do |workflow|
+    workflow.strip!
+    Workflow.require_workflow workflow
+  end
+end
+
+if options[:requires]
+  requires = options[:requires].split(',')
+  requires.each do |req|
+    req.strip!
+    require req
+  end
+end
 # Set task
 namespace = nil, nil
 

data/test/rbbt/entity/test_identifiers.rb

@@ -36,5 +36,37 @@ class TestEntityIdentifiers < Test::Unit::TestCase
     assert_match "hsa", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").to("KEGG Gene ID")
     assert_match "TP53", Gene.setup("ENSG00000141510", "Ensembl Gene ID", "Hsa/feb2014").to("KEGG Gene ID").to(:name)
   end
-end
 
+  def ___test_complex
+
+    file = Path.setup('/home/mvazquezg/git/workflows/PanCancer/share/network/gene_sets/CORUM_protein_complexes.gmt')
+    name = File.basename(file).sub(/\.gmt$/,'')
+    organism = "Hsa/feb2014"
+    key_field = "#{ name } Pathway ID"
+    description_field = "#{name} Pathway Description"
+    description_file = file.find + '.identifiers'
+    tsv = TSV.open(file, :fix => Proc.new{|l| p=l.split"\t"; [p[0], p[1], p[2..-1]*"|"]*"\t"})
+    tsv.namespace = organism
+    tsv.unnamed = true
+    gene_field, count = Organism.guess_id(organism, tsv.values.collect{|l| l.last}.flatten.uniq )
+    tsv.key_field = key_field
+    tsv.fields = [description_field, gene_field]
+    descriptions = tsv.slice(description_field)
+    Open.write(description_file, descriptions.to_single.to_s) #unless File.exists? description_file
+    values = tsv.slice(gene_field)
+    values.identifiers = description_file
+
+    mod = Module.new
+    mod_name = Misc.camel_case(key_field.gsub(/\s+/,'_').sub(/_ID$/,''))
+    Object.const_set(mod_name, mod)
+    mod.instance_eval do
+      extend Entity
+      add_identifiers Path.setup(description_file), key_field, description_field
+      
+      annotation :format
+    end
+    entity = "CORUM:6052"
+    mod.setup(entity, :format => key_field)
+    puts entity.name
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.31
+  version: 5.17.32
 platform: ruby
 authors:
 - Miguel Vazquez