rbbt-util 1.0.1

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Files changed (37) hide show
  1. data/LICENSE +20 -0
  2. data/bin/tchash.rb +15 -0
  3. data/bin/tsv.rb +14 -0
  4. data/lib/rbbt/util/cachehelper.rb +100 -0
  5. data/lib/rbbt/util/cmd.rb +140 -0
  6. data/lib/rbbt/util/data_module.rb +81 -0
  7. data/lib/rbbt/util/excel2tsv.rb +32 -0
  8. data/lib/rbbt/util/filecache.rb +58 -0
  9. data/lib/rbbt/util/log.rb +50 -0
  10. data/lib/rbbt/util/misc.rb +158 -0
  11. data/lib/rbbt/util/open.rb +200 -0
  12. data/lib/rbbt/util/pkg_config.rb +78 -0
  13. data/lib/rbbt/util/pkg_data.rb +110 -0
  14. data/lib/rbbt/util/pkg_software.rb +130 -0
  15. data/lib/rbbt/util/simpleDSL.rb +92 -0
  16. data/lib/rbbt/util/simpleopt.rb +56 -0
  17. data/lib/rbbt/util/tc_hash.rb +124 -0
  18. data/lib/rbbt/util/tmpfile.rb +42 -0
  19. data/lib/rbbt/util/tsv.rb +804 -0
  20. data/lib/rbbt-util.rb +13 -0
  21. data/lib/rbbt.rb +15 -0
  22. data/share/install/software/lib/install_helpers +257 -0
  23. data/test/rbbt/util/test_cmd.rb +30 -0
  24. data/test/rbbt/util/test_data_module.rb +45 -0
  25. data/test/rbbt/util/test_excel2tsv.rb +10 -0
  26. data/test/rbbt/util/test_filecache.rb +36 -0
  27. data/test/rbbt/util/test_misc.rb +22 -0
  28. data/test/rbbt/util/test_open.rb +89 -0
  29. data/test/rbbt/util/test_simpleDSL.rb +55 -0
  30. data/test/rbbt/util/test_simpleopt.rb +10 -0
  31. data/test/rbbt/util/test_tc_hash.rb +18 -0
  32. data/test/rbbt/util/test_tmpfile.rb +20 -0
  33. data/test/rbbt/util/test_tsv.rb +652 -0
  34. data/test/test_helper.rb +9 -0
  35. data/test/test_pkg.rb +38 -0
  36. data/test/test_rbbt.rb +90 -0
  37. metadata +185 -0
data/test/test_rbbt.rb ADDED
@@ -0,0 +1,90 @@
1
+ require File.expand_path(File.dirname(__FILE__) + '/test_helper')
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+ require 'rbbt'
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+ require 'rbbt/util/misc'
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+ require 'rbbt/util/open'
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+
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+ class TestRbbt < Test::Unit::TestCase
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+ def test_url
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+ Rbbt.add_datafiles :test => ['test', 'http://google.com']
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+ assert(Misc.fixutf8(File.open(Rbbt.find_datafile('test')).read) =~ /html/)
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+ FileUtils.rm_rf File.dirname(Rbbt.find_datafile('test'))
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+ end
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+
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+ def test_proc
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+ Rbbt.add_datafiles :test => ['test', proc{'test'}]
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+ assert(Open.read(Rbbt.find_datafile('test')) == 'test')
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+ FileUtils.rm_rf File.dirname(Rbbt.find_datafile('test'))
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+ end
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+
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+ def test_Rakefile
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+ sharedir = PKGData.sharedir_for_file(__FILE__)
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+
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+ FileUtils.rmtree File.join(Rbbt.datadir, 'rake')
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+ FileUtils.mkdir_p File.join(sharedir, 'install', 'rake')
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+ File.open(File.join(sharedir, 'install', 'rake', 'Rakefile'), 'w') do |f|
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+ f.puts "task :default do File.open('foo', 'w') do |f| f.puts 'bar' end end"
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+ end
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+
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+ Rbbt.add_datafiles :rake => ['', 'rake']
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+
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+ assert_equal 'bar', Open.read(File.join(Rbbt.datadir, 'rake', 'foo')).chomp
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+
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+ FileUtils.rmtree File.join(sharedir, 'install', 'rake')
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+ FileUtils.rmtree File.join(Rbbt.datadir, 'rake')
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+ end
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+
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+ def test_Rakefile_with_file
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+ sharedir = PKGData.sharedir_for_file(__FILE__)
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+
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+ FileUtils.mkdir_p File.join(sharedir, 'install', 'rake')
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+ File.open(File.join(sharedir, 'install', 'rake', 'Rakefile'), 'w') do |f|
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+ f.puts "\
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+ task :default do File.open('foo', 'w') do |f| f.puts 'bar' end end
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+ task 'file1' do |t| File.open(t.name, 'w') do |f| f.puts 'file 1' end end
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+ "
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+ end
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+
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+ Rbbt.add_datafiles 'rake/file1' => ['', 'rake']
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+
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+ assert(! File.exists?(File.join(Rbbt.datadir, 'rake', 'foo')))
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+ assert(File.exists?(File.join(Rbbt.datadir, 'rake', 'file1')))
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+ assert_equal('file 1', Open.read(File.join(Rbbt.datadir, 'rake', 'file1')).chomp)
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+ assert_equal('file 1', Open.read(Rbbt.find_datafile('rake/file1')).chomp)
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+
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+ FileUtils.rm_rf File.join(sharedir, 'install', 'rake')
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+ FileUtils.rm_rf File.join(Rbbt.datadir, 'rake')
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+ end
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+
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+ def test_xclip
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+ sharedir = PKGData.sharedir_for_file(__FILE__)
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+
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+ File.open(File.join(sharedir, 'install', 'software', 'xclip'), 'w') do |f|
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+ f.puts '#!/bin/bash
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+
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+ INSTALL_HELPER_FILE="$1"
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+ RBBT_SOFTWARE_DIR="$2"
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+ source "$INSTALL_HELPER_FILE"
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+
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+ name="xclip:0.12"
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+ url="http://downloads.sourceforge.net/project/xclip/xclip/0.12/xclip-0.12.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fxclip%2F&ts=1286472387&use_mirror=sunet"
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+
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+ install_src "$name" "$url"
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+ '
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+ end
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+ FileUtils.chmod 0774, File.join(sharedir, 'install', 'software', 'xclip')
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+
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+ Rbbt.add_software :xclip => ['','']
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+ Rbbt.find_software :xclip
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+ assert File.exists? File.join(Rbbt.bin_dir, 'xclip')
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+
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+ FileUtils.rm_rf File.join(sharedir, 'install', 'software', 'xclip')
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+ Dir.glob(File.join(Rbbt.datadir, 'software', 'opt', 'xclip','bin/*')).each do |exe|
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+ FileUtils.rm_rf File.join(Rbbt.datadir, 'software', 'opt', 'bin', File.basename(exe))
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+ end
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+ Dir.glob(File.join(Rbbt.datadir, 'software', 'opt', 'xclip','current', 'bin/*')).each do |exe|
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+ FileUtils.rm_rf File.join(Rbbt.datadir, 'software', 'opt', 'bin', File.basename(exe))
86
+ end
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+ FileUtils.rm_rf File.join(Rbbt.datadir, 'software', 'opt', 'xclip')
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+ end
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+
90
+ end
metadata ADDED
@@ -0,0 +1,185 @@
1
+ --- !ruby/object:Gem::Specification
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+ name: rbbt-util
3
+ version: !ruby/object:Gem::Version
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+ hash: 21
5
+ prerelease: false
6
+ segments:
7
+ - 1
8
+ - 0
9
+ - 1
10
+ version: 1.0.1
11
+ platform: ruby
12
+ authors:
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+ - Miguel Vazquez
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+ autorequire:
15
+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2010-12-14 00:00:00 +01:00
19
+ default_executable:
20
+ dependencies:
21
+ - !ruby/object:Gem::Dependency
22
+ name: rake
23
+ prerelease: false
24
+ requirement: &id001 !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ">="
28
+ - !ruby/object:Gem::Version
29
+ hash: 3
30
+ segments:
31
+ - 0
32
+ version: "0"
33
+ type: :runtime
34
+ version_requirements: *id001
35
+ - !ruby/object:Gem::Dependency
36
+ name: spreadsheet
37
+ prerelease: false
38
+ requirement: &id002 !ruby/object:Gem::Requirement
39
+ none: false
40
+ requirements:
41
+ - - ">="
42
+ - !ruby/object:Gem::Version
43
+ hash: 3
44
+ segments:
45
+ - 0
46
+ version: "0"
47
+ type: :runtime
48
+ version_requirements: *id002
49
+ - !ruby/object:Gem::Dependency
50
+ name: ruby-prof
51
+ prerelease: false
52
+ requirement: &id003 !ruby/object:Gem::Requirement
53
+ none: false
54
+ requirements:
55
+ - - ">="
56
+ - !ruby/object:Gem::Version
57
+ hash: 3
58
+ segments:
59
+ - 0
60
+ version: "0"
61
+ type: :runtime
62
+ version_requirements: *id003
63
+ - !ruby/object:Gem::Dependency
64
+ name: tokyocabinet
65
+ prerelease: false
66
+ requirement: &id004 !ruby/object:Gem::Requirement
67
+ none: false
68
+ requirements:
69
+ - - ">="
70
+ - !ruby/object:Gem::Version
71
+ hash: 3
72
+ segments:
73
+ - 0
74
+ version: "0"
75
+ type: :runtime
76
+ version_requirements: *id004
77
+ - !ruby/object:Gem::Dependency
78
+ name: progress-monitor
79
+ prerelease: false
80
+ requirement: &id005 !ruby/object:Gem::Requirement
81
+ none: false
82
+ requirements:
83
+ - - ">="
84
+ - !ruby/object:Gem::Version
85
+ hash: 3
86
+ segments:
87
+ - 0
88
+ version: "0"
89
+ type: :runtime
90
+ version_requirements: *id005
91
+ description: Utilities for handling tsv files, caches, etc
92
+ email: miguel.vazquez@fdi.ucm.es
93
+ executables:
94
+ - tsv.rb
95
+ - tchash.rb
96
+ extensions: []
97
+
98
+ extra_rdoc_files:
99
+ - LICENSE
100
+ files:
101
+ - LICENSE
102
+ - lib/rbbt-util.rb
103
+ - lib/rbbt.rb
104
+ - lib/rbbt/util/cachehelper.rb
105
+ - lib/rbbt/util/cmd.rb
106
+ - lib/rbbt/util/data_module.rb
107
+ - lib/rbbt/util/excel2tsv.rb
108
+ - lib/rbbt/util/filecache.rb
109
+ - lib/rbbt/util/log.rb
110
+ - lib/rbbt/util/misc.rb
111
+ - lib/rbbt/util/open.rb
112
+ - lib/rbbt/util/pkg_config.rb
113
+ - lib/rbbt/util/pkg_data.rb
114
+ - lib/rbbt/util/pkg_software.rb
115
+ - lib/rbbt/util/simpleDSL.rb
116
+ - lib/rbbt/util/simpleopt.rb
117
+ - lib/rbbt/util/tc_hash.rb
118
+ - lib/rbbt/util/tmpfile.rb
119
+ - lib/rbbt/util/tsv.rb
120
+ - share/install/software/lib/install_helpers
121
+ - test/rbbt/util/test_cmd.rb
122
+ - test/rbbt/util/test_data_module.rb
123
+ - test/rbbt/util/test_excel2tsv.rb
124
+ - test/rbbt/util/test_filecache.rb
125
+ - test/rbbt/util/test_misc.rb
126
+ - test/rbbt/util/test_open.rb
127
+ - test/rbbt/util/test_simpleDSL.rb
128
+ - test/rbbt/util/test_simpleopt.rb
129
+ - test/rbbt/util/test_tc_hash.rb
130
+ - test/rbbt/util/test_tmpfile.rb
131
+ - test/rbbt/util/test_tsv.rb
132
+ - test/test_helper.rb
133
+ - test/test_pkg.rb
134
+ - test/test_rbbt.rb
135
+ - bin/tsv.rb
136
+ - bin/tchash.rb
137
+ has_rdoc: true
138
+ homepage: http://github.com/mikisvaz/rbbt-util
139
+ licenses: []
140
+
141
+ post_install_message:
142
+ rdoc_options: []
143
+
144
+ require_paths:
145
+ - lib
146
+ required_ruby_version: !ruby/object:Gem::Requirement
147
+ none: false
148
+ requirements:
149
+ - - ">="
150
+ - !ruby/object:Gem::Version
151
+ hash: 3
152
+ segments:
153
+ - 0
154
+ version: "0"
155
+ required_rubygems_version: !ruby/object:Gem::Requirement
156
+ none: false
157
+ requirements:
158
+ - - ">="
159
+ - !ruby/object:Gem::Version
160
+ hash: 3
161
+ segments:
162
+ - 0
163
+ version: "0"
164
+ requirements: []
165
+
166
+ rubyforge_project:
167
+ rubygems_version: 1.3.7
168
+ signing_key:
169
+ specification_version: 3
170
+ summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
171
+ test_files:
172
+ - test/rbbt/util/test_cmd.rb
173
+ - test/rbbt/util/test_data_module.rb
174
+ - test/rbbt/util/test_excel2tsv.rb
175
+ - test/rbbt/util/test_filecache.rb
176
+ - test/rbbt/util/test_misc.rb
177
+ - test/rbbt/util/test_open.rb
178
+ - test/rbbt/util/test_simpleDSL.rb
179
+ - test/rbbt/util/test_simpleopt.rb
180
+ - test/rbbt/util/test_tc_hash.rb
181
+ - test/rbbt/util/test_tmpfile.rb
182
+ - test/rbbt/util/test_tsv.rb
183
+ - test/test_helper.rb
184
+ - test/test_pkg.rb
185
+ - test/test_rbbt.rb