scbi_mapreduce 0.0.40 → 0.0.45

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Files changed (64) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +14 -0
  3. data/Gemfile +4 -0
  4. data/LICENSE.txt +22 -0
  5. data/{README.rdoc → README.md} +0 -0
  6. data/Rakefile +8 -28
  7. data/lib/scbi_mapreduce.rb +2 -10
  8. data/lib/scbi_mapreduce/main_worker.rb +20 -6
  9. data/lib/scbi_mapreduce/manager.rb +4 -0
  10. data/lib/scbi_mapreduce/version.rb +3 -0
  11. data/lib/scbi_mapreduce/work_manager.rb +22 -0
  12. data/lib/scbi_mapreduce/worker_launcher.rb +34 -0
  13. data/scbi_mapreduce.gemspec +27 -0
  14. data/skeleton/.DS_Store +0 -0
  15. data/skeleton/dummy_calcs/.DS_Store +0 -0
  16. data/skeleton/old/dummy_calculations/README.txt +25 -0
  17. data/skeleton/old/dummy_calculations/lib/calculations.rb +37 -0
  18. data/skeleton/old/dummy_calculations/lib/thread_pool.rb +107 -0
  19. data/skeleton/old/dummy_calculations/main.rb +59 -0
  20. data/skeleton/old/dummy_calculations/my_worker.rb +56 -0
  21. data/skeleton/old/dummy_calculations/my_worker_manager.rb +52 -0
  22. data/skeleton/old/dummy_calculations/threads_implementation.rb +29 -0
  23. data/skeleton/old/sequences_blast/README.txt +31 -0
  24. data/{test/drb_test/main.rb → skeleton/old/sequences_blast/launch_only_workers.rb} +6 -10
  25. data/skeleton/old/sequences_blast/lib/db/mids.fasta +64 -0
  26. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nhr +0 -0
  27. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nin +0 -0
  28. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nog +0 -0
  29. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nsd +48 -0
  30. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nsi +0 -0
  31. data/skeleton/old/sequences_blast/lib/db/mids.fasta.nsq +0 -0
  32. data/skeleton/old/sequences_blast/lib/find_mids.rb +134 -0
  33. data/skeleton/old/sequences_blast/lib/thread_pool.rb +107 -0
  34. data/skeleton/old/sequences_blast/linear_implementation.rb +86 -0
  35. data/skeleton/old/sequences_blast/logs/worker0_osiris-2.local_log.txt +13 -0
  36. data/skeleton/old/sequences_blast/logs/worker1_osiris-2.local_log.txt +13 -0
  37. data/skeleton/old/sequences_blast/main.rb +63 -0
  38. data/skeleton/old/sequences_blast/my_worker.rb +58 -0
  39. data/skeleton/old/sequences_blast/my_worker_manager.rb +60 -0
  40. data/skeleton/old/sequences_blast/results.fastq +3996 -0
  41. data/skeleton/old/sequences_blast/test_threads.rb +32 -0
  42. data/skeleton/old/sequences_blast/threads_implementation.rb +108 -0
  43. data/skeleton/remove_mids/lib/db/mids.fasta.nhr +0 -0
  44. data/skeleton/remove_mids/lib/db/mids.fasta.nin +0 -0
  45. data/skeleton/remove_mids/lib/db/mids.fasta.nog +0 -0
  46. data/skeleton/remove_mids/lib/db/mids.fasta.nsd +120 -0
  47. data/skeleton/remove_mids/lib/db/mids.fasta.nsi +0 -0
  48. data/skeleton/remove_mids/lib/db/mids.fasta.nsq +0 -0
  49. data/{.gemtest → skeleton/remove_mids/results.fastq558292} +0 -0
  50. data/skeleton/remove_mids/results.fastq662870 +3996 -0
  51. data/skeleton/simple/launch_only_workers.rb +29 -0
  52. metadata +102 -110
  53. data/History.txt +0 -93
  54. data/Manifest.txt +0 -47
  55. data/PostInstall.txt +0 -7
  56. data/script/console +0 -10
  57. data/script/destroy +0 -14
  58. data/script/generate +0 -14
  59. data/test/drb_test/my_worker.rb +0 -36
  60. data/test/drb_test/my_worker_manager.rb +0 -41
  61. data/test/drb_test/scbi_drb_checkpoint +0 -1
  62. data/test/drb_test/scbi_mapreduce_checkpoint +0 -1
  63. data/test/test_helper.rb +0 -3
  64. data/test/test_scbi_drb.rb +0 -11
data/PostInstall.txt DELETED
@@ -1,7 +0,0 @@
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-
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- For more information on scbi_mapreduce, see http://scbi_mapreduce.rubyforge.org
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-
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- NOTE: Change this information in PostInstall.txt
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- You can also delete it if you don't want it.
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-
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-
data/script/console DELETED
@@ -1,10 +0,0 @@
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- #!/usr/bin/env ruby
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- # File: script/console
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- irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
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-
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- libs = " -r irb/completion"
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- # Perhaps use a console_lib to store any extra methods I may want available in the cosole
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- # libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
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- libs << " -r #{File.dirname(__FILE__) + '/../lib/scbi_mapreduce.rb'}"
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- puts "Loading scbi_mapreduce gem"
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- exec "#{irb} #{libs} --simple-prompt"
data/script/destroy DELETED
@@ -1,14 +0,0 @@
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- #!/usr/bin/env ruby
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- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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-
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- begin
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- require 'rubigen'
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- rescue LoadError
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- require 'rubygems'
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- require 'rubigen'
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- end
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- require 'rubigen/scripts/destroy'
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-
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- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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- RubiGen::Scripts::Destroy.new.run(ARGV)
data/script/generate DELETED
@@ -1,14 +0,0 @@
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- #!/usr/bin/env ruby
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- APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
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-
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- begin
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- require 'rubigen'
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- rescue LoadError
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- require 'rubygems'
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- require 'rubigen'
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- end
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- require 'rubigen/scripts/generate'
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-
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- ARGV.shift if ['--help', '-h'].include?(ARGV[0])
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- RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
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- RubiGen::Scripts::Generate.new.run(ARGV)
data/test/drb_test/my_worker.rb DELETED
@@ -1,36 +0,0 @@
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- # require 'scbi_mapreduce'
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- require 'json'
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-
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- class MyWorker < ScbiMapreduce::Worker
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-
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- def starting_worker
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-
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- # $WORKER_LOG.info "Loading actions"
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- rescue Exception => e
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- puts (e.message+ e.backtrace.join("\n"))
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-
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- end
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-
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-
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- def receive_initial_config(obj)
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-
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- # Reads the parameters
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- # $WORKER_LOG.info "Params received: #{obj.to_json}"
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- @params = obj
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-
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-
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- end
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-
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-
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- def process_object(obj)
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- #return `echo #{obj} | tr aeiou AEIOU`.chomp
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- # sleep 1
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- return obj
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- end
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-
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-
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- def closing_worker
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-
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- end
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- end
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-
data/test/drb_test/my_worker_manager.rb DELETED
@@ -1,41 +0,0 @@
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- require 'json'
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-
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- class MyWorkerManager < ScbiMapreduce::WorkManager
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-
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- def self.init_work_manager
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- @@params = {:algo=> 5}
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- @@datos = 200000
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- # @@fi=File.open(/tmp
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- end
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-
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- def self.end_work_manager
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-
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- end
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-
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- def worker_initial_config
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- return @@params
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- end
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-
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- # this method is called every time a worker needs a new work
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- # Return the work data or nil if no more data is available
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- def next_work
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- @@datos -= 1
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- if (@@datos%10000)==0
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- puts "=> #{@@datos}"
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- end
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-
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- e = @@datos
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- e = nil if @@datos<0
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- return e
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-
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- end
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-
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- def work_received(obj)
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-
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- # puts obj
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- # write_seq_to_disk(seq)
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-
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- end
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-
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- end
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-
data/test/drb_test/scbi_drb_checkpoint DELETED
@@ -1 +0,0 @@
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- 95598
data/test/drb_test/scbi_mapreduce_checkpoint DELETED
@@ -1 +0,0 @@
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- 199909
data/test/test_helper.rb DELETED
@@ -1,3 +0,0 @@
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- require 'stringio'
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- require 'test/unit'
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- require File.dirname(__FILE__) + '/../lib/scbi_mapreduce'
data/test/test_scbi_drb.rb DELETED
@@ -1,11 +0,0 @@
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- require File.dirname(__FILE__) + '/test_helper.rb'
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-
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- class TestScbiDrb < Test::Unit::TestCase
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-
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- def setup
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- end
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-
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- def test_truth
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- assert true
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- end
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- end