rbbt-util 5.9.1 → 5.9.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: f1861d29eec6bc26661f829c80f1aa3367684a69
+  metadata.gz: 74f82edf975ef1ad0c05363e915c57fa2ae1ec43
+  data.tar.gz: f42669bd1035c8734f8425f317ce30f8a0aedbaa
 SHA512:
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-  data.tar.gz: 29cd31366e10b06ce60cd6df50d65067cce46450cddf188f6322fcd5a46c4c71b2a4669ef5521a1f6e21edea0967bf7b2b068e7acef6838bb08f833f377e8e13
+  metadata.gz: 1c8e0ca5a067f5cc2dc79dea4eaba8ebe369509ac5f23b24740ebcdddc80cf9bd2b7ee78b19359f8b5382ff27a40c5a92285f0450919e87b6209935c20996f60
+  data.tar.gz: d617993ba70c9cb43a5aa9ba176da9994db0493aafc484831b68bb7c1804f34ffff3a7f88c2342d21d3b06cfd4a5db08014e033cd90915669e6cd7b56625f18f

data/bin/rbbt

@@ -16,11 +16,15 @@ $ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value
 --locate_file           #{Log.color :yellow, "Report the location of the script instead of executing it"}
 EOF
 
-Log.nocolor = true if options[:nocolor]
+if options[:nocolor]
+  Log.nocolor = true 
+end
+
 locate = options.delete :locate_file
 
 if options[:log]
   Log.severity = options[:log].to_i
+  SOPT.input_descriptions.each{|t,d| d.replace Log.uncolor(d) }
 end
 
 if options[:command_dir]

data/lib/rbbt/tsv.rb

@@ -159,10 +159,4 @@ module TSV
 
     data
   end
-
-  def self.traverse_old(file, options, &block)
-    return file.through(options[:key_field], options[:fields], &block) if TSV === file
-
-    TSV::Parser.traverse(TSV.get_stream(file), options, &block)
-  end
 end

data/lib/rbbt/tsv/attach.rb

@@ -222,4 +222,10 @@ module TSV
       tsv
     end
   end
+
+  def merge_zip(other)
+    other.each do |k,v|
+      self.zip_new k, v
+    end
+  end
 end

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -14,6 +14,20 @@ module TSV
     end
   end
 
+  def self.traverse_hash(hash, options = {}, &block)
+    callback = Misc.process_options options, :callback
+
+    if callback
+      hash.each do |k,v|
+        callback.call yield(k,v)
+      end
+    else
+      hash.each do |k,v|
+        yield k,v 
+      end
+    end
+  end
+
   def self.traverse_array(array, options = {}, &block)
     callback = Misc.process_options options, :callback
 
@@ -38,6 +52,8 @@ module TSV
     case obj
     when TSV
       traverse_tsv(obj, options, &block)
+    when Hash
+      traverse_hash(obj, options, &block)
     when IO
       callback = Misc.process_options options, :callback
       if callback
@@ -48,6 +64,10 @@ module TSV
       else
         TSV::Parser.traverse(obj, options, &block)
       end
+    when Path
+      obj.open do |stream|
+        traverse_obj(stream, options, &block)
+      end
     when Array
       traverse_array(obj, options, &block)
     else
@@ -102,12 +122,20 @@ module TSV
   def self.store_into(obj, value)
     case obj
     when Hash
+      return if value.nil?
       if Hash === value
-        obj.merge! value
+        if TSV === obj and obj.type == :double
+          obj.merge_zip value
+        else
+          obj.merge! value
+        end
       else
         k,v = value
         obj[k] = v
       end
+    when IO
+      return if value.nil?
+      obj << value
     else
       obj << value
     end 

data/lib/rbbt/tsv/parser.rb

@@ -474,7 +474,7 @@ module TSV
             key, values = self.get_values parts
             values = self.cast_values values if self.cast?
             
-            yield key, values, self
+            yield key, values
 
             line = stream.gets
             line_num += 1

data/lib/rbbt/workflow/doc.rb

@@ -46,6 +46,7 @@ module Workflow
   def load_documentation
     @documentation = Workflow.parse_workflow_doc documentation_markdown
     @documentation[:tasks].each do |task, description|
+      raise "Documentation for #{ task }, but not a #{ self.to_s } task" unless tasks.include? task.to_sym
       tasks[task.to_sym].description = description
     end
   end

data/lib/rbbt/workflow/usage.rb

@@ -58,7 +58,9 @@ module Workflow
       puts
 
       tasks.each do |name,task|
-        puts Misc.format_definition_list_item(name.to_s, task.description || "", 80, 30, :yellow)
+        description = task.description || ""
+        description = description.split("\n\n").first
+        puts Misc.format_definition_list_item(name.to_s, description, 80, 30, :yellow)
       end
 
     else

data/share/rbbt_commands/file_server/add

@@ -1,6 +1,23 @@
 #!/usr/bin/env ruby
 
-require 'rbbt'
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Sets a file server for a particular resource
+
+$ rbbt file_server add <Resource> <URL>
+
+It sets the entry in #{Rbbt.etc.file_servers.find}
+
+E.g. rbbt file_server add Organism http://<server>:<port>
+
+-h--help Print this help
+
+EOF
+rbbt_usage and exit 0 if options[:help]
 
 resource, url = ARGV
 

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -66,6 +66,20 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
+  def test_traverse_stream_cpus
+    require 'rbbt/sources/organism'
+
+    head = 100
+
+    tsv = Organism.identifiers("Hsa")
+    res = {}
+    TSV.traverse tsv, :head => head, :cpus => 5, :into => res do |k,v|
+      [k,v]
+    end
+
+    assert_equal head, res.keys.compact.sort.length
+  end
+
   def test_traverse_stream_keys
     require 'rbbt/sources/organism'
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.1
+  version: 5.9.2
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -318,7 +318,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)