rbbt-util 5.5.15 → 5.5.16

checksums.yaml

@@ -1,15 +1,7 @@
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+SHA1:
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+  data.tar.gz: 6ad90f2f6b51247751b4dd6ee3c1d0d7f64d964e
+SHA512:
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+  data.tar.gz: aa40ce6bb8dff89c493956ee95a1504ee6ebac35e436df8861f0a6eb63d32406545f1f968025c148e11b6d55aa4c4efbb8fc096d85580af0aaced5cc35c4e03a

data/etc/app.d/base.rb

@@ -2,7 +2,7 @@
 register Sinatra::RbbtRESTMain
 register Sinatra::RbbtRESTEntity
 register Sinatra::RbbtRESTWorkflow
-register Sinatra::RbbtRESTFileServer
+register Sinatra::RbbtRESTFileServer # Remove to prevent serving files
 register Sinatra::RbbtRESTKnowledgeBase
 helpers Sinatra::RbbtMiscHelpers
 

data/lib/rbbt/association.rb

@@ -67,10 +67,12 @@ module Association
   #{{{ Open
   
   def self.open_tsv(file, source, source_header, target, target_header, all_fields, options)
-    fields = all_fields.dup
+    fields = Misc.process_options options, :fields
+    fields ||= all_fields.dup
+
     fields.delete source 
     fields.delete target
-    fields.unshift target
+    fields.unshift target 
 
     open_options = options.merge({
       :persist => false,
@@ -156,21 +158,31 @@ module Association
     end
 
     if fields and all_fields
-      field_pos = fields.collect{|f| Fixnum === f ? f : fields.index(f) }
+      field_pos = fields.collect{|f| Fixnum === f ? f : all_fields.index(f) }
       fields = all_fields.values_at *field_pos
     else
-      fields = all_fields[1..-1] if all_fields
+      #fields = all_fields[1..-1] if all_fields
     end
 
-    source, source_header, orig_source_format = calculate_headers(key_field, fields, source_spec)
+    source, source_header, orig_source_format = calculate_headers(key_field, fields || all_fields, source_spec)
     source_format ||= orig_source_format 
     source = key_field if source.nil? 
     source = key_field if source == :key
     source_header ||= source
 
-    target, target_header, orig_target_format = calculate_headers(key_field, fields, target_spec)
+    target, target_header, orig_target_format = calculate_headers(key_field, fields || all_fields, target_spec)
     target_format ||= orig_target_format 
-    target = (key_field == source ? fields.first : (([key_field] + fields) - [source]).first) if target.nil?
+    if target.nil?
+      target = case
+               when fields
+                 fields.first
+               when key_field == source
+                 all_fields[1]
+               else
+                 (([key_field] + all_fields) - [source]).first
+               end
+    end
+
     target = key_field if target == :key
     target_header ||= target
 
@@ -185,7 +197,7 @@ module Association
       target_format ||= format[_type] if format.include? _type 
     end
 
-    [source, source_header, source_format, target, target_header, target_format]
+    [source, source_header, source_format, target, target_header, target_format, fields || all_fields]
   end
 
   def self.load_tsv(file, options)
@@ -200,13 +212,13 @@ module Association
       key_field, *fields = all_fields = TSV.parse_header(file, options.merge(:fields => nil, :key_field => nil)).all_fields
     end
 
-    source, source_header, source_format, target, target_header, target_format = specs(all_fields, options)
+    source, source_header, source_format, target, target_header, target_format, fields = specs(all_fields, options)
  
     Log.low("Loading associations from: #{ Misc.fingerprint file }")
     Log.low("sources: #{ [source, source_header, source_format].join(", ") }")
     Log.low("targets: #{ [target, target_header, target_format].join(", ") }")
 
-    tsv = open_tsv(file, source, source_header, target, target_header, all_fields, options)
+    tsv = open_tsv(file, source, source_header, target, target_header, all_fields, options.merge(:fields => fields.dup))
 
     tsv = translate_tsv(tsv, source_format, target_format)
 

data/lib/rbbt/resource/util.rb

@@ -48,7 +48,7 @@ module Resource
 
       begin
         if not File.exists? File.join(opt_dir,'.post_install')
-          Open.write(File.join(opt_dir,'.post_install'),"#!/bin/bash\n")
+          #Open.write(File.join(opt_dir,'.post_install'),"#!/bin/bash\n")
         end
       rescue Exception
         Log.warn("Could not create default .post_install in #{ software_dir }")

data/lib/rbbt/workflow.rb

@@ -71,7 +71,7 @@ module Workflow
     else
       case
         # Points to workflow file
-      when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb') or File.exists?(wf_name))
+      when ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb'))
         filename = (wf_name =~ /\.?\//) ? wf_name : "./" << wf_name 
       when (defined?(Rbbt) and Rbbt.etc.workflow_dir.exists?)
         dir = Rbbt.etc.workflow_dir.read.strip

data/share/rbbt_commands/install/workflow

@@ -1,5 +1,6 @@
 #!/usr/bin/env ruby
 
+require 'rbbt'
 require 'rbbt-util'
 require 'rbbt/workflow'
 

data/test/rbbt/test_association.rb

@@ -6,8 +6,8 @@ require 'rbbt/entity'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-
-Workflow.require_workflow "TSVWorkflow"
+Workflow.require_workflow "Genomics"
+require 'rbbt/entity/gene'
 
 TEST_ASSOCIATIONS =<<-EOF
 #: :sep=" "#:namespace=Hsa/jan2013

data/test/rbbt/test_knowledge_base.rb

@@ -50,6 +50,25 @@ class TestKnowledgeBase < Test::Unit::TestCase
     assert @kb.all_databases.include? "pina"
   end
 
+  def test_items
+    tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
+    kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
+    kb.index('g2t', Organism.gene_transcripts("Hsa/jan2013"), :target => "Ensembl Transcript ID")
+  end
+
+  def __test_subset
+    gene = "TP53"
+    found = Genomics.knowledge_base.identify :pina, gene
+    p53_interactors = Misc.profile{ Genomics.knowledge_base.children(:pina, found).target_entity }
+
+
+    Misc.profile do
+      puts Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).length
+    end
+    ddd 2
+    #assert Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).target_entities.name.include? "MDM2"
+  end
+
   def test_benchmark
     tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
     kb = KnowledgeBase.new Rbbt.tmp.test.kb2
@@ -69,12 +88,6 @@ class TestKnowledgeBase < Test::Unit::TestCase
       end
   end
 
-  def test_items
-    tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
-    kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
-    kb.index('g2t', Organism.gene_transcripts("Hsa/jan2013"), :target => "Ensembl Transcript ID")
-  end
-
   def test_benchmark2
     tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
     kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
@@ -86,19 +99,6 @@ class TestKnowledgeBase < Test::Unit::TestCase
     assert l > 0
   end
 
-  def __test_subset
-    gene = "TP53"
-    found = Genomics.knowledge_base.identify :pina, gene
-    p53_interactors = Misc.profile{ Genomics.knowledge_base.children(:pina, found).target_entity }
-
-
-    Misc.profile do
-      puts Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).length
-    end
-    ddd 2
-    #assert Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).target_entities.name.include? "MDM2"
-  end
-
   def test_syndication
     kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
     kb.syndicate @kb, :genomics

metadata

@@ -1,55 +1,55 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.15
+  version: 5.5.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-04 00:00:00.000000000 Z
+date: 2013-11-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: lockfile
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
@@ -161,40 +161,40 @@ files:
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - README.rdoc
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/test_fix_width_table.rb
 - test/rbbt/association/test_index.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_soap.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_annotations.rb
+- test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_cmd.rb
 - test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/test_rbbt.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
 - test/test_helper.rb
+- test/test_rbbt.rb
 - bin/tsv.rb
 - bin/tchash.rb
 - bin/run_workflow.rb
@@ -213,12 +213,12 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
@@ -228,37 +228,37 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/test_fix_width_table.rb
 - test/rbbt/association/test_index.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_soap.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_annotations.rb
+- test/rbbt/test_association.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_cmd.rb
 - test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/test_rbbt.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
 - test/test_helper.rb
+- test/test_rbbt.rb