scout-gear 9.0.0 → 10.0.1

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Files changed (129) hide show
  1. checksums.yaml +4 -4
  2. data/.vimproject +3 -3
  3. data/Rakefile +1 -2
  4. data/VERSION +1 -1
  5. data/bin/scout +0 -1
  6. data/lib/rbbt-scout.rb +2 -1
  7. data/lib/scout/offsite/exceptions.rb +9 -0
  8. data/lib/scout/offsite/ssh.rb +1 -0
  9. data/lib/scout/semaphore.rb +2 -0
  10. data/lib/scout/tsv/dumper.rb +1 -0
  11. data/lib/scout/tsv/open.rb +8 -2
  12. data/lib/scout/tsv/parser.rb +1 -1
  13. data/lib/scout/tsv/persist/adapter.rb +2 -2
  14. data/lib/scout/tsv/persist.rb +1 -0
  15. data/lib/scout/tsv/util.rb +1 -1
  16. data/lib/scout/tsv.rb +1 -1
  17. data/lib/scout/work_queue/exceptions.rb +18 -0
  18. data/lib/scout/work_queue.rb +1 -0
  19. data/lib/scout/workflow/definition.rb +1 -1
  20. data/lib/scout/workflow/step/config.rb +1 -1
  21. data/lib/scout/workflow/step/dependencies.rb +3 -2
  22. data/lib/scout/workflow/step/file.rb +5 -1
  23. data/lib/scout/workflow/step/info.rb +8 -2
  24. data/lib/scout/workflow/step/provenance.rb +28 -10
  25. data/lib/scout/workflow/step/status.rb +4 -0
  26. data/lib/scout/workflow/step.rb +18 -6
  27. data/lib/scout/workflow/task/dependencies.rb +1 -0
  28. data/lib/scout/workflow/task/inputs.rb +6 -1
  29. data/lib/scout/workflow/task.rb +22 -3
  30. data/lib/scout/workflow/usage.rb +1 -0
  31. data/lib/scout/workflow.rb +13 -4
  32. data/lib/scout-gear.rb +1 -10
  33. data/scout-gear.gemspec +8 -98
  34. data/scout_commands/workflow/task +2 -3
  35. data/test/scout/workflow/step/test_provenance.rb +24 -1
  36. data/test/scout/workflow/task/test_inputs.rb +0 -4
  37. metadata +7 -110
  38. data/lib/scout/cmd.rb +0 -347
  39. data/lib/scout/concurrent_stream.rb +0 -284
  40. data/lib/scout/config.rb +0 -168
  41. data/lib/scout/exceptions.rb +0 -151
  42. data/lib/scout/indiferent_hash/case_insensitive.rb +0 -30
  43. data/lib/scout/indiferent_hash/options.rb +0 -115
  44. data/lib/scout/indiferent_hash.rb +0 -96
  45. data/lib/scout/log/color.rb +0 -224
  46. data/lib/scout/log/color_class.rb +0 -269
  47. data/lib/scout/log/fingerprint.rb +0 -69
  48. data/lib/scout/log/progress/report.rb +0 -244
  49. data/lib/scout/log/progress/util.rb +0 -173
  50. data/lib/scout/log/progress.rb +0 -106
  51. data/lib/scout/log/trap.rb +0 -107
  52. data/lib/scout/log.rb +0 -441
  53. data/lib/scout/meta_extension.rb +0 -100
  54. data/lib/scout/misc/digest.rb +0 -63
  55. data/lib/scout/misc/filesystem.rb +0 -25
  56. data/lib/scout/misc/format.rb +0 -255
  57. data/lib/scout/misc/helper.rb +0 -31
  58. data/lib/scout/misc/insist.rb +0 -56
  59. data/lib/scout/misc/monitor.rb +0 -66
  60. data/lib/scout/misc/system.rb +0 -73
  61. data/lib/scout/misc.rb +0 -10
  62. data/lib/scout/named_array.rb +0 -138
  63. data/lib/scout/open/lock/lockfile.rb +0 -587
  64. data/lib/scout/open/lock.rb +0 -68
  65. data/lib/scout/open/remote.rb +0 -135
  66. data/lib/scout/open/stream.rb +0 -491
  67. data/lib/scout/open/util.rb +0 -244
  68. data/lib/scout/open.rb +0 -170
  69. data/lib/scout/path/find.rb +0 -204
  70. data/lib/scout/path/tmpfile.rb +0 -8
  71. data/lib/scout/path/util.rb +0 -107
  72. data/lib/scout/path.rb +0 -51
  73. data/lib/scout/persist/open.rb +0 -17
  74. data/lib/scout/persist/path.rb +0 -15
  75. data/lib/scout/persist/serialize.rb +0 -157
  76. data/lib/scout/persist.rb +0 -104
  77. data/lib/scout/resource/open.rb +0 -8
  78. data/lib/scout/resource/path.rb +0 -80
  79. data/lib/scout/resource/produce/rake.rb +0 -69
  80. data/lib/scout/resource/produce.rb +0 -151
  81. data/lib/scout/resource/scout.rb +0 -3
  82. data/lib/scout/resource/software.rb +0 -178
  83. data/lib/scout/resource/util.rb +0 -55
  84. data/lib/scout/resource.rb +0 -41
  85. data/lib/scout/simple_opt/accessor.rb +0 -54
  86. data/lib/scout/simple_opt/doc.rb +0 -126
  87. data/lib/scout/simple_opt/get.rb +0 -57
  88. data/lib/scout/simple_opt/parse.rb +0 -67
  89. data/lib/scout/simple_opt/setup.rb +0 -26
  90. data/lib/scout/simple_opt.rb +0 -5
  91. data/lib/scout/tmpfile.rb +0 -129
  92. data/test/scout/indiferent_hash/test_case_insensitive.rb +0 -16
  93. data/test/scout/indiferent_hash/test_options.rb +0 -46
  94. data/test/scout/log/test_progress.rb +0 -108
  95. data/test/scout/misc/test_digest.rb +0 -30
  96. data/test/scout/misc/test_filesystem.rb +0 -30
  97. data/test/scout/misc/test_insist.rb +0 -13
  98. data/test/scout/misc/test_system.rb +0 -21
  99. data/test/scout/open/test_lock.rb +0 -52
  100. data/test/scout/open/test_remote.rb +0 -25
  101. data/test/scout/open/test_stream.rb +0 -676
  102. data/test/scout/open/test_util.rb +0 -73
  103. data/test/scout/path/test_find.rb +0 -119
  104. data/test/scout/path/test_util.rb +0 -22
  105. data/test/scout/persist/test_open.rb +0 -37
  106. data/test/scout/persist/test_path.rb +0 -37
  107. data/test/scout/persist/test_serialize.rb +0 -114
  108. data/test/scout/resource/test_path.rb +0 -46
  109. data/test/scout/resource/test_produce.rb +0 -77
  110. data/test/scout/resource/test_software.rb +0 -24
  111. data/test/scout/resource/test_util.rb +0 -27
  112. data/test/scout/simple_opt/test_doc.rb +0 -16
  113. data/test/scout/simple_opt/test_get.rb +0 -11
  114. data/test/scout/simple_opt/test_parse.rb +0 -10
  115. data/test/scout/simple_opt/test_setup.rb +0 -77
  116. data/test/scout/test_cmd.rb +0 -85
  117. data/test/scout/test_concurrent_stream.rb +0 -29
  118. data/test/scout/test_config.rb +0 -66
  119. data/test/scout/test_indiferent_hash.rb +0 -26
  120. data/test/scout/test_log.rb +0 -32
  121. data/test/scout/test_meta_extension.rb +0 -80
  122. data/test/scout/test_misc.rb +0 -6
  123. data/test/scout/test_named_array.rb +0 -43
  124. data/test/scout/test_open.rb +0 -146
  125. data/test/scout/test_path.rb +0 -54
  126. data/test/scout/test_persist.rb +0 -186
  127. data/test/scout/test_resource.rb +0 -26
  128. data/test/scout/test_tmpfile.rb +0 -53
  129. /data/test/scout/{log/test_color.rb → test_offsite.rb} +0 -0
@@ -1,151 +0,0 @@
1
- require_relative '../open'
2
- require_relative '../tmpfile'
3
- require_relative 'produce/rake'
4
-
5
- module Resource
6
- def claim(path, type, content = nil, &block)
7
- if type == :rake
8
- @rake_dirs ||= {}
9
- @rake_dirs[path] = content || block
10
- else
11
- @resources ||= {}
12
- @resources[path] = [type, content || block]
13
- end
14
- end
15
-
16
- def rake_for(path)
17
- @rake_dirs ||= {}
18
- @rake_dirs.select{|dir, content|
19
- Misc.path_relative_to(dir, path)
20
- }.sort_by{|dir, content|
21
- dir.length
22
- }.last
23
- end
24
-
25
- def has_rake(path)
26
- !! rake_for(path)
27
- end
28
-
29
- def run_rake(path, rakefile, rake_dir)
30
- task = Misc.path_relative_to rake_dir, path
31
- rakefile = rakefile.produce if rakefile.respond_to? :produce
32
- rakefile = rakefile.find if rakefile.respond_to? :find
33
-
34
- rake_dir = rake_dir.find(:user) if rake_dir.respond_to? :find
35
-
36
- begin
37
- if Proc === rakefile
38
- ScoutRake.run(nil, rake_dir, task, &rakefile)
39
- else
40
- ScoutRake.run(rakefile, rake_dir, task)
41
- end
42
- rescue ScoutRake::TaskNotFound
43
- if rake_dir.nil? or rake_dir.empty? or rake_dir == "/" or rake_dir == "./"
44
- raise $!
45
- end
46
- task = File.join(File.basename(rake_dir), task)
47
- rake_dir = File.dirname(rake_dir)
48
- retry
49
- end
50
- end
51
-
52
- def produce(path, force = false)
53
- case
54
- when (@resources && @resources.include?(path))
55
- type, content = @resources[path]
56
- when (Path === path && @resources && @resources.include?(path.original))
57
- type, content = @resources[path.original]
58
- when has_rake(path)
59
- type = :rake
60
- rake_dir, content = rake_for(path)
61
- rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
62
- else
63
- if path !~ /\.(gz|bgz)$/
64
- begin
65
- produce(path.annotate(path + '.gz'), force)
66
- rescue ResourceNotFound
67
- begin
68
- produce(path.annotate(path + '.bgz'), force)
69
- rescue ResourceNotFound
70
- raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
71
- end
72
- end
73
- else
74
- raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
75
- end
76
- end
77
-
78
- if path.respond_to?(:find)
79
- final_path = force ? path.find(:default) : path.find
80
- else
81
- final_path = path
82
- end
83
-
84
- if type and not File.exist?(final_path) or force
85
- Log.medium "Producing: (#{self.to_s}) #{ final_path }"
86
- lock_filename = TmpFile.tmp_for_file(final_path, :dir => lock_dir)
87
-
88
- Open.lock lock_filename do
89
- FileUtils.rm_rf final_path if force and File.exist? final_path
90
-
91
- if ! File.exist?(final_path) || force
92
-
93
- begin
94
- case type
95
- when :string
96
- Open.sensible_write(final_path, content)
97
- when :csv
98
- raise "TSV/CSV Not implemented yet"
99
- #require 'rbbt/tsv/csv'
100
- #tsv = TSV.csv Open.open(content)
101
- #Open.sensible_write(final_path, tsv.to_s)
102
- when :url
103
- options = {}
104
- options[:noz] = true if Open.gzip?(final_path) || Open.bgzip?(final_path) || Open.zip?(final_path)
105
- Open.sensible_write(final_path, Open.open(content, options))
106
- when :proc
107
- data = case content.arity
108
- when 0
109
- content.call
110
- when 1
111
- content.call final_path
112
- end
113
- case data
114
- when String, IO, StringIO
115
- Open.sensible_write(final_path, data)
116
- when Array
117
- Open.sensible_write(final_path, data * "\n")
118
- when TSV
119
- Open.sensible_write(final_path, data.dumper_stream)
120
- when TSV::Dumper
121
- Open.sensible_write(final_path, data.stream)
122
- when nil
123
- else
124
- raise "Unkown object produced: #{Log.fingerprint data}"
125
- end
126
- when :rake
127
- run_rake(path, content, rake_dir)
128
- when :install
129
- software_dir = self.root.software
130
- name = File.basename(path)
131
- Resource.install(content, name, software_dir)
132
- set_software_env(software_dir)
133
- else
134
- raise "Could not produce #{ resource }. (#{ type }, #{ content })"
135
- end
136
- rescue
137
- FileUtils.rm_rf final_path if File.exist? final_path
138
- raise $!
139
- end
140
- end
141
- end
142
- end
143
-
144
- # After producing a file, make sure we recheck all locations, the file
145
- # might have appeared with '.gz' extension for instance
146
- path.instance_variable_set("@path", {})
147
-
148
- path
149
- end
150
-
151
- end
@@ -1,3 +0,0 @@
1
- module Scout
2
- extend Resource
3
- end
@@ -1,178 +0,0 @@
1
- module Resource
2
-
3
- def self.install_helpers
4
- File.expand_path(Scout.share.software.install_helpers.find(:lib))
5
- end
6
-
7
- def self.install(content, name, software_dir = Path.setup('software'), &block)
8
- software_dir ||= Path.setup('software')
9
- software_dir = software_dir.find(:user) if Path === software_dir
10
-
11
- content = block if block_given?
12
-
13
- preamble = <<-EOF
14
- #!/bin/bash
15
-
16
- SOFTWARE_DIR="#{software_dir}"
17
-
18
- INSTALL_HELPER_FILE="#{install_helpers}"
19
- source "$INSTALL_HELPER_FILE"
20
- EOF
21
-
22
- content = content.call if Proc === content
23
-
24
- name = content[:name] if Hash === content && content.include?(:name)
25
- content =
26
- if content =~ /git:|\.git$/
27
- {:git => content}
28
- else
29
- {:src => content}
30
- end if String === content and Open.remote?(content)
31
-
32
- script_text =
33
- case content
34
- when nil
35
- raise "No way to install #{name}"
36
- when Path
37
- Open.read(content)
38
- when String
39
- if Path.is_filename?(content) and Open.exists?(content)
40
- Open.read(content)
41
- else
42
- content
43
- end
44
- when Hash
45
- name = content[:name] || name
46
- git = content[:git]
47
- src = content[:src]
48
- url = content[:url]
49
- jar = content[:jar]
50
- extra = content[:extra]
51
- commands = content[:commands]
52
- if git
53
- <<-EOF
54
-
55
- name='#{name}'
56
- url='#{git}'
57
-
58
- install_git "$name" "$url" #{extra}
59
-
60
- #{commands}
61
- EOF
62
- elsif src
63
- <<-EOF
64
-
65
- name='#{name}'
66
- url='#{src}'
67
-
68
- install_src "$name" "$url" #{extra}
69
-
70
- #{commands}
71
- EOF
72
- elsif jar
73
- <<-EOF
74
-
75
- name='#{name}'
76
- url='#{jar}'
77
-
78
- install_jar "$name" "$url" #{extra}
79
-
80
- #{commands}
81
- EOF
82
- else
83
- <<-EOF
84
-
85
- name='#{name}'
86
- url='#{url}'
87
-
88
- #{commands}
89
- EOF
90
- end
91
- end
92
-
93
- script = preamble + "\n" + script_text
94
- Log.debug "Installing software #{name} into #{software_dir} with script:\n" << script
95
- CMD.cmd_log('bash', :in => script)
96
- Resource.set_software_env(software_dir)
97
- end
98
-
99
- def self.set_software_env(software_dir = Path.setup('software'))
100
- software_dir.opt.find_all.collect{|d| d.annotate(File.dirname(d)) }.reverse.each do |software_dir|
101
- next unless software_dir.exists?
102
- Log.medium "Preparing software env at #{software_dir}"
103
-
104
- software_dir = File.expand_path(software_dir)
105
- opt_dir = File.join(software_dir, 'opt')
106
- bin_dir = File.join(opt_dir, 'bin')
107
-
108
- Misc.env_add 'PATH', bin_dir
109
-
110
- FileUtils.mkdir_p opt_dir unless File.exist? opt_dir
111
-
112
- %w(.ld-paths .c-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
113
- filename = File.join(opt_dir, file)
114
- begin
115
- FileUtils.touch filename unless File.exist? filename
116
- rescue
117
- Log.warn("Could not touch #{ filename }")
118
- end
119
- end
120
-
121
- Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
122
- dir = line.chomp
123
- dir = File.join(opt_dir, dir) unless dir[0] == "/"
124
- Misc.env_add('CPLUS_INCLUDE_PATH',dir)
125
- Misc.env_add('C_INCLUDE_PATH',dir)
126
- end if File.exist? File.join(opt_dir, '.c-paths')
127
-
128
- Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
129
- dir = line.chomp
130
- dir = File.join(opt_dir, dir) unless dir[0] == "/"
131
- Misc.env_add('LIBRARY_PATH',dir)
132
- Misc.env_add('LD_LIBRARY_PATH',dir)
133
- Misc.env_add('LD_RUN_PATH',dir)
134
- end if File.exist? File.join(opt_dir, '.ld-paths')
135
-
136
- Open.read(File.join opt_dir, '.pkgconfig-paths').split(/\n/).each do |line|
137
- dir = line.chomp
138
- dir = File.join(opt_dir, dir) unless dir[0] == "/"
139
- Misc.env_add('PKG_CONFIG_PATH',dir)
140
- end if File.exist? File.join(opt_dir, '.pkgconfig-paths')
141
-
142
- Open.read(File.join opt_dir, '.aclocal-paths').split(/\n/).each do |line|
143
- dir = line.chomp
144
- dir = File.join(opt_dir, dir) unless dir[0] == "/"
145
- Misc.env_add('ACLOCAL_FLAGS', "-I #{dir}", ' ')
146
- end if File.exist? File.join(opt_dir, '.aclocal-paths')
147
-
148
- Open.read(File.join opt_dir, '.java-classpaths').split(/\n/).each do |line|
149
- dir = line.chomp
150
- dir = File.join(opt_dir, dir) unless dir[0] == "/"
151
- Misc.env_add('CLASSPATH', "#{dir}")
152
- end if File.exist? File.join(opt_dir, '.java-classpaths')
153
-
154
- Dir.glob(File.join opt_dir, 'jars', '*.jar').each do |file|
155
- Misc.env_add('CLASSPATH', "#{file}")
156
- end
157
-
158
- if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
159
- Dir.glob(File.join(opt_dir, '.post_install','*')).each do |file|
160
-
161
- # Load exports
162
- Open.read(file).split("\n").each do |line|
163
- next unless line =~ /^\s*export\s+([^=]+)=(.*)/
164
- var = $1.strip
165
- value = $2.strip
166
- value.sub!(/^['"]/,'')
167
- value.sub!(/['"]$/,'')
168
- value.gsub!(/\$[a-z_0-9]+/i){|var| ENV[var[1..-1]] }
169
- Log.debug "Set variable export from .post_install: #{Log.fingerprint [var,value]*"="}"
170
- ENV[var] = value
171
- end
172
- end
173
- end
174
- end
175
- end
176
-
177
- self.set_software_env
178
- end
@@ -1,55 +0,0 @@
1
- module Resource
2
- def identify(path)
3
- return path unless path.start_with?("/")
4
- path_maps = path.path_maps if Path === path
5
- path_maps ||= self.path_maps || Path.path_maps
6
- path = File.expand_path(path)
7
- path += "/" if File.directory?(path)
8
-
9
- map_order ||= (path_maps.keys & Path.basic_map_order) + (path_maps.keys - Path.basic_map_order)
10
- map_order -= [:current, "current"]
11
-
12
- choices = []
13
- map_order.uniq.each do |name|
14
- pattern = path_maps[name]
15
- pattern = path_maps[pattern] while Symbol === pattern
16
- next if pattern.nil?
17
-
18
- pattern = pattern.sub('{PWD}', Dir.pwd)
19
- pattern = pattern.sub('{HOME}', ENV["HOME"])
20
- if String === pattern and pattern.include?('{')
21
- regexp = "^" + pattern
22
- .gsub(/{(TOPLEVEL)}/,'(?<\1>[^/]+)')
23
- .gsub(/{([^}]+)}/,'(?<\1>[^/]+)?') +
24
- "(?:/(?<REST>.*))?/?$"
25
- if m = path.match(regexp)
26
- if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == self.pkgdir
27
- unlocated = %w(TOPLEVEL SUBPATH PATH REST).collect{|c|
28
- m.named_captures.include?(c) ? m[c] : nil
29
- }.compact * "/"
30
- unlocated.gsub!(/\/+/,'/')
31
- unlocated[self.subdir] = "" if self.subdir
32
- choices << self.annotate(unlocated)
33
- end
34
- end
35
- end
36
- end
37
-
38
- identified = choices.sort_by{|s| s.length }.first
39
-
40
- Path.setup(identified || path, self, nil, path_maps)
41
- end
42
-
43
- def self.identify(path)
44
- resource = path.pkgdir if Path === path
45
- resource = Scout unless Resource === resource
46
- unlocated = resource.identify path
47
- end
48
-
49
- def self.relocate(path)
50
- return path if Open.exists?(path)
51
- unlocated = identify(path)
52
- unlocated.find
53
- end
54
- end
55
-
@@ -1,41 +0,0 @@
1
- require_relative 'log'
2
- require_relative 'path'
3
- require_relative 'resource/produce'
4
- require_relative 'resource/path'
5
- require_relative 'resource/open'
6
- require_relative 'resource/util'
7
- require_relative 'resource/software'
8
-
9
- module Resource
10
- extend MetaExtension
11
- extension_attr :pkgdir, :libdir, :subdir, :resources, :rake_dirs, :path_maps, :lock_dir
12
-
13
- def self.default_lock_dir
14
- Path.setup('tmp/produce_locks').find
15
- end
16
-
17
- def subdir
18
- @subdir ||= ""
19
- end
20
-
21
- def lock_dir
22
- @lock_dir ||= Resource.default_lock_dir
23
- end
24
-
25
- def pkgdir
26
- @pkgdir ||= Path.default_pkgdir
27
- end
28
-
29
- def root
30
- Path.setup(subdir, self, self.libdir, @path_maps)
31
- end
32
-
33
- def method_missing(name, prev = nil, *args)
34
- if prev.nil?
35
- root.send(name, *args)
36
- else
37
- root.send(name, prev, *args)
38
- end
39
- end
40
- end
41
-
@@ -1,54 +0,0 @@
1
- module SOPT
2
- class << self
3
- attr_writer :inputs, :input_shortcuts, :input_types, :input_descriptions, :input_defaults
4
- end
5
-
6
- def self.all
7
- @all ||= {}
8
- end
9
-
10
- def self.shortcuts
11
- @shortcuts ||= {}
12
- end
13
-
14
- def self.inputs
15
- @inputs ||= []
16
- end
17
-
18
- def self.input_shortcuts
19
- @input_shortcuts ||= {}
20
- end
21
-
22
- def self.input_types
23
- @input_types ||= {}
24
- end
25
-
26
- def self.input_descriptions
27
- @input_descriptions ||= {}
28
- end
29
-
30
- def self.input_defaults
31
- @input_defaults ||= {}
32
- end
33
-
34
- def self.reset
35
- @shortcuts = {}
36
- @all = {}
37
- end
38
-
39
- def self.delete_inputs(inputs)
40
- inputs.each do |input|
41
- input = input.to_s
42
- self.shortcuts.delete self.input_shortcuts.delete(input)
43
- self.inputs.delete input
44
- self.input_types.delete input
45
- self.input_defaults.delete input
46
- self.input_descriptions.delete input
47
- end
48
- end
49
-
50
- def self.usage
51
- puts SOPT.doc
52
- exit 0
53
- end
54
- end
@@ -1,126 +0,0 @@
1
- require_relative '../log'
2
- module SOPT
3
-
4
- class << self
5
- attr_writer :command, :summary, :synopsys, :description
6
- end
7
-
8
- def self.command
9
- @command ||= File.basename($0)
10
- end
11
-
12
- def self.summary
13
- @summary ||= ""
14
- end
15
-
16
- def self.synopsys
17
- @synopsys ||= begin
18
- "#{command} " <<
19
- inputs.collect{|name|
20
- "[" << input_format(name, input_types[name] || :string, input_defaults[name], input_shortcuts[name]).sub(/:$/,'') << "]"
21
- } * " "
22
- end
23
- end
24
-
25
- def self.description
26
- @description ||= "Missing"
27
- end
28
-
29
- def self.input_format(name, type = nil, default = nil, short = nil)
30
- input_str = (short.nil? or short.empty?) ? "--#{name}" : "-#{short},--#{name}"
31
- input_str = Log.color(:blue, input_str)
32
- extra = case type
33
- when nil
34
- ""
35
- when :boolean
36
- "[=false]"
37
- when :tsv, :text
38
- "=<file|->"
39
- when :array
40
- "=<list|file|->"
41
- else
42
- "=<#{ type }>"
43
- end
44
- #extra << " (default: #{Array === default ? (default.length > 3 ? default[0..2]*", " + ', ...' : default*", " ): default})" if default != nil
45
- extra << " (default: #{Log.fingerprint(default)})" if default != nil
46
- input_str << Log.color(:green, extra)
47
- end
48
-
49
- def self.input_array_doc(input_array)
50
- input_array.collect do |name,type,description,default,options|
51
- type = :string if type.nil?
52
-
53
- name = name.to_s
54
- shortcut, options = options, nil if String === options || Symbol === options
55
-
56
- case options && options[:shortcut]
57
- when FalseClass
58
- shortcut = nil
59
- when TrueClass, nil
60
- shortcut = fix_shortcut(name[0], name)
61
- else
62
- shortcut = options[:shortcut]
63
- end unless shortcut
64
-
65
- shortcut = fix_shortcut(shortcut, name)
66
- register(shortcut, name, type, description) unless self.inputs.include? name
67
- name = SOPT.input_format(name, type.to_sym, default, shortcut )
68
- Misc.format_definition_list_item(name, description)
69
- end * "\n"
70
- end
71
-
72
- def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
73
- type = description = default = nil
74
- shortcut = ""
75
- seen = []
76
- inputs.collect do |name|
77
- next if seen.include? name
78
- seen << name
79
-
80
- type = input_types[name] unless input_types.nil?
81
- description = input_descriptions[name] unless input_descriptions.nil?
82
- default = input_defaults[name] unless input_defaults.nil?
83
-
84
- name = name.to_s
85
-
86
- case input_shortcuts
87
- when nil, FalseClass
88
- shortcut = nil
89
- when Hash
90
- shortcut = input_shortcuts[name]
91
- when TrueClass
92
- shortcut = fix_shortcut(name[0], name)
93
- end
94
-
95
- type = :string if type.nil?
96
- register(shortcut, name, type, description) unless self.inputs.include? name
97
-
98
- name = SOPT.input_format(name, type.to_sym, default, shortcut)
99
- Misc.format_definition_list_item(name, description)
100
- end * "\n"
101
- end
102
-
103
-
104
- def self.doc
105
- doc =<<-EOF
106
- #{Log.color :magenta}#{command}(1) -- #{summary}
107
- #{"=" * (command.length + summary.length + 7)}#{Log.color :reset}
108
-
109
- EOF
110
-
111
- if synopsys and not synopsys.empty?
112
- doc << Log.color(:magenta, "## SYNOPSYS") << "\n\n"
113
- doc << Log.color(:blue, synopsys) << "\n\n"
114
- end
115
-
116
- if description and not description.empty?
117
- doc << Log.color(:magenta, "## DESCRIPTION") << "\n\n"
118
- doc << Misc.format_paragraph(description) << "\n\n"
119
- end
120
-
121
- doc << Log.color(:magenta, "## OPTIONS") << "\n\n"
122
- doc << input_doc(inputs, input_types, input_descriptions, input_defaults, input_shortcuts)
123
-
124
- doc
125
- end
126
- end
@@ -1,57 +0,0 @@
1
- module SOPT
2
- GOT_OPTIONS= IndiferentHash.setup({})
3
- def self.current_options=(options)
4
- @@current_options = options
5
- end
6
- def self.consume(args = ARGV)
7
- i = 0
8
- @@current_options ||= {}
9
- while i < args.length do
10
- current = args[i]
11
- break if current == "--"
12
- if m = current.match(/--?(.+?)(?:=(.+))?$/)
13
- key = $1
14
- value = $2
15
-
16
- input = inputs.include?(key)? key : shortcuts[key]
17
-
18
- if input.nil?
19
- i += 1
20
- next
21
- else
22
- args.delete_at i
23
- end
24
- else
25
- i += 1
26
- next
27
- end
28
-
29
- if input_types[input] == :string
30
- value = args.delete_at(i) if value.nil?
31
- @@current_options[input] = value
32
- else
33
- if value.nil? and %w(F false FALSE no).include?(args[i])
34
- Log.warn "Boolean values are best specified as #{current}=[true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value"
35
- value = args.delete_at(i)
36
- end
37
- @@current_options[input] = %w(F false FALSE no).include?(value)? false : true
38
- end
39
- end
40
-
41
- IndiferentHash.setup @@current_options
42
- GOT_OPTIONS.merge! @@current_options
43
-
44
- @@current_options
45
- end
46
-
47
- def self.get(opt_str)
48
- SOPT.parse(opt_str)
49
- SOPT.consume(ARGV)
50
- end
51
-
52
- def self.require(options, *parameters)
53
- parameters.flatten.each do |parameter|
54
- raise ParameterException, "Parameter '#{ Log.color :blue, parameter }' not given" if options[parameter].nil?
55
- end
56
- end
57
- end