rbbt-util 4.3.0 → 4.4.0
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- data/README.rdoc +11 -6
- data/bin/rbbt_exec.rb +9 -1
- data/lib/rbbt/annotations.rb +78 -22
- data/lib/rbbt/persist.rb +14 -6
- data/lib/rbbt/persist/tsv.rb +10 -4
- data/lib/rbbt/resource.rb +1 -0
- data/lib/rbbt/resource/path.rb +43 -2
- data/lib/rbbt/resource/util.rb +3 -3
- data/lib/rbbt/tsv.rb +8 -2
- data/lib/rbbt/tsv/accessor.rb +29 -28
- data/lib/rbbt/tsv/attach.rb +8 -3
- data/lib/rbbt/tsv/attach/util.rb +3 -0
- data/lib/rbbt/tsv/excel.rb +91 -0
- data/lib/rbbt/tsv/filter.rb +17 -7
- data/lib/rbbt/tsv/manipulate.rb +26 -11
- data/lib/rbbt/tsv/parser.rb +3 -3
- data/lib/rbbt/tsv/util.rb +6 -29
- data/lib/rbbt/util/R.rb +27 -2
- data/lib/rbbt/util/chain_methods.rb +1 -2
- data/lib/rbbt/util/misc.rb +142 -13
- data/lib/rbbt/util/named_array.rb +5 -5
- data/lib/rbbt/util/open.rb +8 -4
- data/lib/rbbt/workflow.rb +5 -40
- data/lib/rbbt/workflow/accessor.rb +11 -0
- data/lib/rbbt/workflow/annotate.rb +8 -2
- data/lib/rbbt/workflow/step.rb +21 -2
- data/lib/rbbt/workflow/task.rb +3 -3
- data/share/lib/R/util.R +48 -15
- data/test/rbbt/resource/test_path.rb +15 -0
- data/test/rbbt/test_annotations.rb +11 -1
- data/test/rbbt/test_tsv.rb +15 -2
- data/test/rbbt/tsv/test_index.rb +27 -24
- data/test/rbbt/tsv/test_util.rb +1 -0
- data/test/rbbt/util/test_misc.rb +20 -0
- data/test/rbbt/util/test_open.rb +3 -5
- data/test/rbbt/workflow/test_step.rb +2 -2
- metadata +24 -9
data/test/rbbt/tsv/test_util.rb
CHANGED
data/test/rbbt/util/test_misc.rb
CHANGED
@@ -4,6 +4,26 @@ require 'test/unit'
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class TestMisc < Test::Unit::TestCase
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def test_fixutf8
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8
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string = "abc\xffdef"
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9
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string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
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assert(! string.valid_encoding?) if string.respond_to? :valid_encoding?
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assert(! string.valid_encoding) if string.respond_to? :valid_encoding
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12
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assert( Misc.fixutf8(string).valid_encoding?) if string.respond_to? :valid_encoding?
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assert( Misc.fixutf8(string).valid_encoding) if string.respond_to? :valid_encoding
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end
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def test_colors_for
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colors, used = Misc.colors_for([1,2,2,1,2,1,2,2,3,3,2,3,2])
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assert_equal Misc::COLOR_LIST[1], used[2]
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end
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def test_total_length
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ranges = [(0..100), (50..150), (120..160)]
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ranges = [(0..100), (50..150), (120..160), (51..70)]
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assert_equal 161, Misc.total_length(ranges)
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end
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def test_id_filename?
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TmpFile.with_file("") do |file|
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assert Misc.is_filename?(file)
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data/test/rbbt/util/test_open.rb
CHANGED
@@ -13,15 +13,13 @@ class TestOpen < Test::Unit::TestCase
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def test_nice
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nice = 0.5
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Open.wget('http://google.com', :quiet => true, :nice => nice).read =~ /html/
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t = Time.now
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Open.wget('http://google.com', :quiet => true, :nice => nice).read
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Open.wget('http://google.com', :quiet => true, :nice => nice).read
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assert(Time.now - t + 0.5 >= nice)
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Open.wget('http://google.com', :quiet => true, :nice => nice, :nice_key => 1).read
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Open.wget('http://google.com', :quiet => true, :nice => nice, :nice_key => 2).read =~ /html/
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Open.wget('http://google.com', :quiet => true, :nice => nice, :nice_key => 1).read
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t = Time.now
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Open.wget('http://google.com', :quiet => true, :nice => nice, :nice_key => 1).read
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Open.wget('http://google.com', :quiet => true, :nice => nice, :nice_key => 1).read
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assert(Time.now - t + 0.5 >= nice)
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end
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@@ -3,7 +3,7 @@ require 'rbbt/workflow/task'
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require 'rbbt/workflow/step'
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require 'rbbt'
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-
class
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class TestStep < Test::Unit::TestCase
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def test_step
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task = Task.setup do "TEST" end
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@@ -86,7 +86,7 @@ class TestStrp < Test::Unit::TestCase
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while not job.abort do sleep 1 end
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Open.write(lock, "open")
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job.join
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assert job.
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assert job.aborted?
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end
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end
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end
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metadata
CHANGED
@@ -1,13 +1,13 @@
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1
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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-
hash:
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hash: 47
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prerelease:
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segments:
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- 4
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-
-
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- 4
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- 0
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version: 4.
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version: 4.4.0
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platform: ruby
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authors:
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- Miguel Vazquez
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@@ -15,7 +15,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-
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date: 2012-07-18 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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@@ -129,6 +129,20 @@ dependencies:
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version: "0"
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type: :runtime
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version_requirements: *id008
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- !ruby/object:Gem::Dependency
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name: simplews
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prerelease: false
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requirement: &id009 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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hash: 3
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segments:
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- 0
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version: "0"
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type: :runtime
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version_requirements: *id009
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description: Utilities for handling tsv files, caches, etc
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email: miguel.vazquez@cnio.es
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executables:
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@@ -160,6 +174,7 @@ files:
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- lib/rbbt/tsv/accessor.rb
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- lib/rbbt/tsv/attach.rb
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- lib/rbbt/tsv/attach/util.rb
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- lib/rbbt/tsv/excel.rb
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- lib/rbbt/tsv/filter.rb
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- lib/rbbt/tsv/index.rb
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- lib/rbbt/tsv/manipulate.rb
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@@ -191,9 +206,9 @@ files:
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- test/test_helper.rb
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- test/rbbt/util/test_tmpfile.rb
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- test/rbbt/util/test_filecache.rb
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- test/rbbt/util/test_open.rb
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/test_misc.rb
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/test_open.rb
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- test/rbbt/util/test_cmd.rb
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- test/rbbt/util/test_simpleDSL.rb
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- test/rbbt/util/test_chain_methods.rb
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@@ -251,7 +266,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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requirements: []
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rubyforge_project:
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rubygems_version: 1.8.
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rubygems_version: 1.8.24
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signing_key:
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specification_version: 3
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summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
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@@ -259,9 +274,9 @@ test_files:
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- test/test_helper.rb
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- test/rbbt/util/test_tmpfile.rb
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- test/rbbt/util/test_filecache.rb
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- test/rbbt/util/test_open.rb
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/test_misc.rb
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- test/rbbt/util/test_R.rb
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- test/rbbt/util/test_open.rb
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- test/rbbt/util/test_cmd.rb
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- test/rbbt/util/test_simpleDSL.rb
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- test/rbbt/util/test_chain_methods.rb
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