rbbt-util 5.5.1 → 5.5.2

checksums.yaml

@@ -1,15 +1,15 @@
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data/lib/rbbt/tsv/accessor.rb

@@ -537,7 +537,15 @@ end
 
   def value_peek
     peek = {}
-    keys[0..10].zip(values[0..10]).each do |k,v| peek[k] = v end
+    i = 0
+    begin
+      through do |k,v|
+        peek[k] = v 
+        i += 1
+        raise "STOP" if i > 10
+      end
+    rescue
+    end
     peek
   end
 

data/lib/rbbt/tsv/util.rb

@@ -126,6 +126,7 @@ module TSV
       end
     end
     self.annotate(new)
+    new.fields = new.fields[0..0] if new.fields
     new.type = :flat
     new
   end

data/lib/rbbt/util/R.rb

@@ -22,7 +22,7 @@ source('#{UTIL}');
       cmd << command
     end
 
-    Log.debug "R Script:\n#{ cmd }"
+    Log.debug{"R Script:\n#{ cmd }"}
 
     if options.delete :monitor
       io = CMD.cmd('R --vanilla --slave --quiet', options.merge(:in => cmd, :pipe => true))
@@ -35,19 +35,16 @@ source('#{UTIL}');
     end
   end
 
-  def self.interactive(init_file, options = {})
-    CMD.cmd("env R_PROFILE='#{init_file}' xterm R")
-  end
-
   def self.interactive(script, options = {})
     TmpFile.with_file do |init_file|
         Open.write(init_file) do |file|
           file.puts "# Loading basic rbbt environment"
+          file.puts "library(utils);\n"
           file.puts "source('#{R::UTIL}');\n"
           file.puts 
           file.puts script
         end
-        CMD.cmd("env R_PROFILE='#{init_file}' xterm R")
+        CMD.cmd("env R_PROFILE='#{init_file}' xterm \"$RHOME/bin/R\"")
     end
   end
 
@@ -98,10 +95,14 @@ if (! is.null(data)){ rbbt.tsv.write('#{f}', data); }
     end
   end
 
-  def R_interactive(open_options = {})
+  def R_interactive(pre_script = nil)
     TmpFile.with_file do |f|
-      Open.write(f, self.to_s)
-      R.interactive("data_file = '#{f}';\n")
+      TmpFile.with_file(pre_script) do |script_file|
+        Open.write(f, self.to_s)
+        script = "data_file = '#{f}';\n"
+        script << "script_file = '#{script_file}';\n" if pre_script
+        R.interactive(script)
+      end
     end
   end
 end

data/lib/rbbt/util/cmd.rb

@@ -29,10 +29,10 @@ module CMD
         rescue
         end
 
-        Log.debug "Process #{ cmd } succeded" if $? and $?.success? and log
+        Log.debug{"Process #{ cmd } succeded" if $? and $?.success? and log}
 
         if $? and not $?.success?
-          Log.debug "Raising exception" if log
+          Log.debug{"Raising exception" if log}
           exception = CMDError.new "Command [#{@pid}] #{@cmd} failed with error status #{$?.exitstatus}"
           original_close
           raise exception
@@ -52,7 +52,7 @@ module CMD
 
     def force_close
       if @pid
-        Log.debug "Forcing close by killing '#{@pid}'" if log
+        Log.debug{"Forcing close by killing '#{@pid}'" if log}
         begin
           Process.kill("KILL", @pid)
           Process.waitpid(@pid)
@@ -158,8 +158,8 @@ module CMD
 
         exit(-1)
       rescue Exception
-        Log.debug("CMDError: #{$!.message}") if log
-        Log.debug("Backtrace: \n" + $!.backtrace * "\n") if log
+        Log.debug{ "CMDError: #{$!.message}" } if log
+        Log.debug{ "Backtrace: \n" + $!.backtrace * "\n" } if log
         raise CMDError, $!.message
       end
     }
@@ -173,7 +173,7 @@ module CMD
     serr = serr.first
     
 
-    Log.debug "CMD: [#{pid}] #{cmd}" if log
+    Log.debug{"CMD: [#{pid}] #{cmd}" if log}
 
     if in_content.respond_to?(:read)
       Thread.new do

data/lib/rbbt/util/log.rb

@@ -17,12 +17,15 @@ module Log
     @logfile = nil
   end
 
-  SEVERITY_COLOR = ["0;37m", "0;32m", "0;33m", "0;31m","0;37m", "0;32m", "0;33m"].collect{|e| "\033[#{e}"}
+  WHITE, DARK, GREEN, YELLOW, RED = ["0;37m", "0m", "0;32m", "0;33m", "0;31m"].collect{|e| "\033[#{e}"}
+
+  SEVERITY_COLOR = [WHITE, GREEN, YELLOW, RED,WHITE, GREEN, YELLOW].collect{|e| "\033[#{e}"}
 
   def self.log(message = nil, severity = MEDIUM, &block)
     message ||= block
+    return if message.nil?
     severity_color = SEVERITY_COLOR[severity]
-    font_color = {false => "\033[0;37m", true => "\033[0m"}[severity >= INFO]
+    font_color = {true => WHITE, false => DARK}[severity >= INFO]
 
     return if severity < self.severity
     message = message.call if Proc === message

data/lib/rbbt/util/misc.rb

@@ -46,7 +46,7 @@ module Misc
       when (ref.length == 1 and m.length == 1)
         m
       else
-        Log.debug "Cannot understand: #{[ref, m]} (#{ muts })"
+        Log.debug{"Cannot understand: #{[ref, m]} (#{ muts })"}
         '-' * ref.length + m
       end
     end
@@ -223,11 +223,11 @@ module Misc
       end
     when TSV
       obj.with_unnamed do
-        "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << "," << fingerprint(obj.keys).inspect << "}"
+        "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << ";" << fingerprint(obj.keys).inspect << "}"
       end
     when Hash
       if obj.length > 10
-        "H:{"<< fingerprint(obj.keys) << "," << fingerprint(obj.values) << "}"
+        "H:{"<< fingerprint(obj.keys) << ";" << fingerprint(obj.values) << "}"
       else
         new = "{"
         obj.each do |k,v|
@@ -941,6 +941,7 @@ end
     return false
   end
 
+  # WARN: probably not thread safe...
   def self.in_dir(dir)
     old_pwd = FileUtils.pwd
     res = nil
@@ -948,8 +949,6 @@ end
       FileUtils.mkdir_p dir unless File.exists? dir
       FileUtils.cd dir
       res = yield
-    rescue
-      raise $!
     ensure
       FileUtils.cd old_pwd
     end

data/lib/rbbt/util/simpleopt.rb

@@ -166,7 +166,7 @@ module SOPT
 
       if shortcuts.include? short
         i[:short] = short_for(i[:long])
-        Log.debug("Short for #{ long } is taken. Changed to #{i[:short]}")
+        Log.debug{ "Short for #{ long } is taken. Changed to #{i[:short]}" }
       else
         shortcuts << i[:short] if short
       end

data/lib/rbbt/workflow.rb

@@ -38,10 +38,10 @@ module Workflow
     begin
       $LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))
       require filename
-      Log.info "Workflow loaded from: #{ filename }"
+      Log.debug{"Workflow loaded from: #{ filename }"}
       return true
     rescue Exception
-      Log.warn "Error loading workflow: #{ filename }"
+      Log.warn{"Error loading workflow: #{ filename }"}
       raise $!
     end
   end
@@ -86,7 +86,7 @@ module Workflow
     # Already loaded
     begin
       Misc.string2const wf_name
-      Log.debug "Workflow #{ wf_name } already loaded"
+      Log.debug{"Workflow #{ wf_name } already loaded"}
       return true
     rescue Exception
     end
@@ -97,13 +97,14 @@ module Workflow
       if Hash === remote_workflows and remote_workflows.include?(wf_name)
         url = remote_workflows[wf_name]
         require_remote_workflow(wf_name, url)
-        Log.debug "Workflow #{ wf_name } loaded remotely: #{ url }"
+        Log.debug{"Workflow #{ wf_name } loaded remotely: #{ url }"}
         return
       end
     end
 
     # Load locally
 
+    Log.info{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) || require_local_workflow(Misc.snake_case(wf_name)) || raise("Workflow not found or could not be loaded: #{ wf_name }")
   end
 

data/lib/rbbt/workflow/accessor.rb

@@ -26,11 +26,13 @@ class Step
   def info
     return {} if not Open.exists? info_file
     begin
-      Open.open(info_file) do |file|
-        INFO_SERIALIAZER.load(file) || {}
+      Misc.insist(2, 0.5) do
+        Open.open(info_file) do |file|
+          INFO_SERIALIAZER.load(file) || {}
+        end
       end
     rescue Exception
-      Log.debug "Error loading info file: " + info_file
+      Log.debug{"Error loading info file: " + info_file}
       raise $!
     end
   end

data/lib/rbbt/workflow/step.rb

@@ -77,10 +77,10 @@ class Step
       self
     else
       begin
-        Log.debug "Waiting for pid: #{@pid}"
+        Log.debug{"Waiting for pid: #{@pid}"}
         Process.waitpid @pid 
       rescue Errno::ECHILD
-        Log.debug "Process #{ @pid } already finished: #{ path }"
+        Log.debug{"Process #{ @pid } already finished: #{ path }"}
       end if Misc.pid_exists? @pid
       @pid = nil
     end
@@ -176,7 +176,7 @@ class Step
         begin
           run(true)
         rescue Step::Aborted
-          Log.debug("Forked process aborted: #{@path}")
+          Log.debug{"Forked process aborted: #{@path}"}
           log :aborted, "Aborted"
           raise $!
         rescue Exception

data/share/rbbt_commands/app/start

@@ -12,8 +12,6 @@ app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : R
 
 app_dir = app_dir[app]
 
-ddd app_dir
-
 server = options[:server] || 'thin'
 Misc.in_dir(app_dir) do
   require 'rack'

data/test/rbbt/association/test_index.rb

@@ -3,11 +3,11 @@ require 'rbbt/workflow'
 require 'rbbt/association'
 require 'rbbt/association/index'
 
-Workflow.require_workflow "Genomics"
-require 'rbbt/entity/gene'
 class TestAssociationIndex < Test::Unit::TestCase
 
   def setup
+    Workflow.require_workflow "Genomics"
+    require 'rbbt/entity/gene'
   end
 
   def teardown

data/test/rbbt/test_association.rb

@@ -6,8 +6,6 @@ require 'rbbt/entity'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 
-Workflow.require_workflow "Genomics"
-require 'rbbt/entity/gene'
 
 Workflow.require_workflow "TSVWorkflow"
 
@@ -35,18 +33,18 @@ class TestAssociations < Test::Unit::TestCase
     FileUtils.rm_rf DAssocs
   end
 
-  def _test_simple_open
+  def test_simple_open
     database = Association.open(FAssocs, {}, :dir => DAssocs)
     assert_equal ["C", "K"], database["c"]["Entity2"]
   end
  
-  def _test_source_open
+  def test_source_open
     database = Association.open(FAssocs, {:source => "Entity2", :zipped => true}, :dir => DAssocs)
     assert_equal ["c", "3", 'cc', "PTEN"], database["C"].flatten
     assert_equal ["c", "4", 'kk', "PTEN"], database["K"].flatten
   end
   
-  def _test_target_open
+  def test_target_open
     database = Association.open(FAssocs, {:source => "Entity2", :target => "Entity3", :zipped => true}, :dir => DAssocs)
     assert_equal ["cc", "c", "3", "PTEN"], database["C"].flatten
     assert_equal ["kk", "c", "4", "PTEN"], database["K"].flatten
@@ -71,24 +69,24 @@ class TestAssociations < Test::Unit::TestCase
   end
 
 
-  def _test_gene_open
+  def test_gene_open
     database = Association.open(FAssocs, {:source => "Gene=~Associated Gene Name", :target => "Entity3", :zipped => true}, :dir => DAssocs)
     assert_equal ["aa"], database["TP53"].first
   end
 
-  def _test_gene_open_translate
+  def test_gene_open_translate
     tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013")
     database = Association.open(FAssocs, {:source => "Gene=~Associated Gene Name", :source_format => "Ensembl Gene ID", :target => "Entity3", :zipped => true}, :dir => DAssocs)
     assert_equal ["aa"], database[tp53.ensembl].first
   end
 
-  def _test_gene_target_open_translate
+  def test_gene_target_open_translate
     tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013")
     database = Association.open(FAssocs, {:target => "Gene=~Associated Gene Name=>Ensembl Gene ID", :source => "Entity3", :zipped => true}, :dir => DAssocs)
     assert_equal [tp53.ensembl], database["aa"].first
   end
 
-  def _test_ICGC
+  def test_ICGC
     assoc = Association.open(Open.open('ftp://data.dcc.icgc.org/current/Chronic_Lymphocytic_Leukemia-ISC_MICINN-ES/simple_somatic_mutation.CLLE-ES.tsv.gz'),
                          { :source => "gene_affected=~Ensembl Gene ID=>Associated Gene Name", :target => "icgc_donor_id=~Sample", 
                            :fields => ['consequence_type'],  

data/test/rbbt/test_knowledge_base.rb

@@ -4,12 +4,13 @@ require 'test/unit'
 require 'rbbt/knowledge_base'
 require 'rbbt/sources/pina'
 
-require 'rbbt/workflow'
-Workflow.require_workflow "Genomics"
-require 'genomics_kb'
-
 class TestKnowledgeBase < Test::Unit::TestCase
   def setup
+    require 'rbbt/workflow'
+    Workflow.require_workflow "Genomics"
+    require 'genomics_kb'
+
+
     KnowledgeBase.knowledge_base_dir = Rbbt.tmp.knowledge_base_test.find
     @kb = Genomics.knowledge_base
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.1
+  version: 5.5.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-21 00:00:00.000000000 Z
+date: 2013-10-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake