scout-gear 7.2.0 → 8.0.0

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Files changed (112) hide show
  1. checksums.yaml +4 -4
  2. data/.vimproject +51 -6
  3. data/VERSION +1 -1
  4. data/bin/scout +6 -3
  5. data/lib/rbbt-scout.rb +1 -0
  6. data/lib/scout/cmd.rb +1 -1
  7. data/lib/scout/concurrent_stream.rb +33 -29
  8. data/lib/scout/config.rb +1 -1
  9. data/lib/scout/exceptions.rb +1 -0
  10. data/lib/scout/log/color.rb +4 -2
  11. data/lib/scout/log/progress/report.rb +1 -1
  12. data/lib/scout/log/progress/util.rb +71 -2
  13. data/lib/scout/log/progress.rb +1 -1
  14. data/lib/scout/log/trap.rb +107 -0
  15. data/lib/scout/log.rb +56 -21
  16. data/lib/scout/meta_extension.rb +13 -6
  17. data/lib/scout/misc/digest.rb +1 -1
  18. data/lib/scout/misc/format.rb +12 -0
  19. data/lib/scout/misc/helper.rb +31 -0
  20. data/lib/scout/misc/insist.rb +1 -1
  21. data/lib/scout/misc/monitor.rb +12 -1
  22. data/lib/scout/misc/system.rb +10 -0
  23. data/lib/scout/misc.rb +1 -0
  24. data/lib/scout/named_array.rb +65 -3
  25. data/lib/scout/open/lock/lockfile.rb +587 -0
  26. data/lib/scout/open/lock.rb +28 -2
  27. data/lib/scout/open/remote.rb +4 -0
  28. data/lib/scout/open/stream.rb +111 -42
  29. data/lib/scout/open/util.rb +13 -3
  30. data/lib/scout/path/find.rb +9 -1
  31. data/lib/scout/path/util.rb +35 -0
  32. data/lib/scout/persist/serialize.rb +18 -5
  33. data/lib/scout/persist.rb +60 -30
  34. data/lib/scout/resource/path.rb +53 -0
  35. data/lib/scout/resource/produce.rb +0 -8
  36. data/lib/scout/resource/util.rb +2 -1
  37. data/lib/scout/semaphore.rb +8 -1
  38. data/lib/scout/tmpfile.rb +7 -8
  39. data/lib/scout/tsv/attach.rb +177 -0
  40. data/lib/scout/tsv/change_id.rb +40 -0
  41. data/lib/scout/tsv/dumper.rb +85 -54
  42. data/lib/scout/tsv/index.rb +188 -20
  43. data/lib/scout/tsv/open.rb +182 -0
  44. data/lib/scout/tsv/parser.rb +200 -118
  45. data/lib/scout/tsv/path.rb +5 -6
  46. data/lib/scout/tsv/persist/adapter.rb +26 -37
  47. data/lib/scout/tsv/persist/fix_width_table.rb +327 -0
  48. data/lib/scout/tsv/persist/serialize.rb +117 -0
  49. data/lib/scout/tsv/persist/tokyocabinet.rb +6 -3
  50. data/lib/scout/tsv/persist.rb +4 -2
  51. data/lib/scout/tsv/transformer.rb +141 -0
  52. data/lib/scout/tsv/traverse.rb +136 -37
  53. data/lib/scout/tsv/util/filter.rb +312 -0
  54. data/lib/scout/tsv/util/process.rb +73 -0
  55. data/lib/scout/tsv/util/reorder.rb +81 -0
  56. data/lib/scout/tsv/util/select.rb +265 -0
  57. data/lib/scout/tsv/util/unzip.rb +86 -0
  58. data/lib/scout/tsv/util.rb +126 -19
  59. data/lib/scout/tsv.rb +28 -5
  60. data/lib/scout/work_queue/socket.rb +6 -1
  61. data/lib/scout/work_queue/worker.rb +5 -2
  62. data/lib/scout/work_queue.rb +15 -8
  63. data/lib/scout/workflow/definition.rb +29 -2
  64. data/lib/scout/workflow/step/dependencies.rb +24 -4
  65. data/lib/scout/workflow/step/info.rb +40 -5
  66. data/lib/scout/workflow/step/progress.rb +14 -0
  67. data/lib/scout/workflow/step/provenance.rb +8 -7
  68. data/lib/scout/workflow/step/status.rb +45 -0
  69. data/lib/scout/workflow/step.rb +104 -33
  70. data/lib/scout/workflow/task/inputs.rb +14 -20
  71. data/lib/scout/workflow/task.rb +86 -47
  72. data/lib/scout/workflow/usage.rb +10 -6
  73. data/scout-gear.gemspec +30 -3
  74. data/scout_commands/workflow/task +37 -9
  75. data/scout_commands/workflow/task_old +2 -2
  76. data/test/scout/open/test_stream.rb +61 -59
  77. data/test/scout/path/test_find.rb +10 -1
  78. data/test/scout/resource/test_produce.rb +15 -0
  79. data/test/scout/test_meta_extension.rb +25 -0
  80. data/test/scout/test_named_array.rb +18 -0
  81. data/test/scout/test_persist.rb +67 -0
  82. data/test/scout/test_tmpfile.rb +1 -1
  83. data/test/scout/test_tsv.rb +222 -3
  84. data/test/scout/test_work_queue.rb +21 -18
  85. data/test/scout/tsv/persist/test_adapter.rb +11 -1
  86. data/test/scout/tsv/persist/test_fix_width_table.rb +134 -0
  87. data/test/scout/tsv/persist/test_tokyocabinet.rb +29 -1
  88. data/test/scout/tsv/test_attach.rb +227 -0
  89. data/test/scout/tsv/test_change_id.rb +98 -0
  90. data/test/scout/tsv/test_dumper.rb +1 -1
  91. data/test/scout/tsv/test_index.rb +127 -3
  92. data/test/scout/tsv/test_open.rb +167 -0
  93. data/test/scout/tsv/test_parser.rb +45 -3
  94. data/test/scout/tsv/test_persist.rb +9 -0
  95. data/test/scout/tsv/test_transformer.rb +108 -0
  96. data/test/scout/tsv/test_traverse.rb +195 -3
  97. data/test/scout/tsv/test_util.rb +24 -0
  98. data/test/scout/tsv/util/test_filter.rb +188 -0
  99. data/test/scout/tsv/util/test_process.rb +47 -0
  100. data/test/scout/tsv/util/test_reorder.rb +94 -0
  101. data/test/scout/tsv/util/test_select.rb +58 -0
  102. data/test/scout/tsv/util/test_unzip.rb +112 -0
  103. data/test/scout/work_queue/test_socket.rb +0 -1
  104. data/test/scout/work_queue/test_worker.rb +63 -6
  105. data/test/scout/workflow/step/test_load.rb +3 -3
  106. data/test/scout/workflow/step/test_status.rb +31 -0
  107. data/test/scout/workflow/task/test_inputs.rb +14 -14
  108. data/test/scout/workflow/test_step.rb +13 -13
  109. data/test/scout/workflow/test_task.rb +168 -32
  110. data/test/scout/workflow/test_usage.rb +33 -6
  111. data/test/test_helper.rb +3 -1
  112. metadata +29 -2
@@ -8,6 +8,13 @@ class TestMetaExtension < Test::Unit::TestCase
8
8
  extension_attr :code, :code2
9
9
  end
10
10
 
11
+ module ExtensionClass2
12
+ extend MetaExtension
13
+
14
+ extension_attr :code3, :code4
15
+ end
16
+
17
+
11
18
  def test_setup_annotate
12
19
  str = "String"
13
20
  ExtensionClass.setup(str, :code)
@@ -51,5 +58,23 @@ class TestMetaExtension < Test::Unit::TestCase
51
58
  assert o.extension_attr_hash.include?(:code)
52
59
  assert o.extension_attr_hash.include?(:code2)
53
60
  end
61
+
62
+ def test_twice
63
+ str = "String"
64
+
65
+ ExtensionClass.setup(str, :code2 => :code)
66
+ assert_equal :code, str.code2
67
+ assert_include str.instance_variable_get(:@extension_attrs), :code
68
+
69
+ str.extend ExtensionClass2
70
+ str.code3 = :code_alt
71
+ assert_equal :code, str.code2
72
+ assert_equal :code_alt, str.code3
73
+ assert_include str.instance_variable_get(:@extension_attrs), :code
74
+ assert_include str.instance_variable_get(:@extension_attrs), :code3
75
+
76
+ assert_include str.extension_attr_hash, :code
77
+ assert_include str.extension_attr_hash, :code3
78
+ end
54
79
  end
55
80
 
@@ -15,5 +15,23 @@ ValueB (Entity type)
15
15
  assert_equal 1, NamedArray.identify_name(names, "ValueB")
16
16
  assert_equal 1, NamedArray.identify_name(names, 1)
17
17
  end
18
+
19
+ def test_missing_field
20
+ a = NamedArray.setup([1,2], [:a, :b])
21
+ assert_equal 1, a[:a]
22
+ assert_equal nil, a[:c]
23
+ end
24
+
25
+ def test_zip_fields
26
+ a = [%w(a b), %w(1 1)]
27
+ assert_equal [%w(a 1), %w(b 1)], NamedArray.zip_fields(a)
28
+ end
29
+
30
+ def test_add_zipped
31
+ a = [%w(a b), %w(1 1)]
32
+ NamedArray.add_zipped a, [%w(c), %w(1)]
33
+ NamedArray.add_zipped a, [%w(d), %w(1)]
34
+ assert_equal [%w(a b c d), %w(1 1 1 1)], a
35
+ end
18
36
  end
19
37
 
@@ -95,6 +95,73 @@ class TestPersist < Test::Unit::TestCase
95
95
  end
96
96
  end
97
97
 
98
+ def test_concurrent
99
+ num = 10
100
+
101
+ s = 0.01
102
+ 10.times do
103
+ TmpFile.with_file do |file|
104
+ output1 = file + '.output1'
105
+ output2 = file + '.output2'
106
+ pid1 = Process.fork do
107
+ Open.purge_pipes
108
+ sleep rand/10.0
109
+ io = Persist.persist("test", :string, :path => file) do
110
+ Open.open_pipe do |sin|
111
+ num.times do |i|
112
+ sin.puts "line-#{i}-#{Process.pid}"
113
+ sleep s
114
+ end
115
+ end
116
+ end
117
+ if IO === io
118
+ Open.consume_stream(io, false)
119
+ else
120
+ Open.write(output1, io)
121
+ end
122
+ end
123
+ pid2 = Process.fork do
124
+ Open.purge_pipes
125
+ sleep rand/10.0
126
+ io = Persist.persist("test", :string, :path => file) do
127
+ Open.open_pipe do |sin|
128
+ num.times do |i|
129
+ sin.puts "line-#{i}-#{Process.pid}"
130
+ sleep s
131
+ end
132
+ end
133
+ end
134
+ if IO === io
135
+ Open.consume_stream(io, false)
136
+ else
137
+ Open.write(output2, io)
138
+ end
139
+ end
140
+ Process.wait
141
+ Process.wait
142
+
143
+ assert File.exist?(output1) || File.exist?(output2)
144
+ [pid1, pid2].zip([output2, output1]).each do |pid, found|
145
+ next unless File.exist?(found)
146
+ assert Open.read(found).include? "-#{pid}\n"
147
+ end
148
+ [pid1, pid2].zip([output1, output2]).each do |pid, found|
149
+ next unless File.exist?(found)
150
+ refute Open.read(found).include? "-#{pid}\n"
151
+ end
152
+ Open.rm file
153
+ Open.rm output1
154
+ Open.rm output2
155
+ end
156
+ end
157
+ end
158
+
159
+ def test_path_prefix
160
+ Persist.persist('foo', :tsv, :prefix => "TSV") do |filename|
161
+ assert File.basename(filename).start_with? "TSV"
162
+ end
163
+ end
164
+
98
165
  def __test_speed
99
166
  times = 100_000
100
167
  TmpFile.with_file do |tmpfile|
@@ -10,7 +10,7 @@ class TestTmpFile < Test::Unit::TestCase
10
10
  def test_do_tmp_file
11
11
  content = "Hello World!"
12
12
  TmpFile.with_file(content) do |file|
13
- assert_equal_path content, File.open(file).read
13
+ assert_equal content, File.open(file).read
14
14
  end
15
15
  end
16
16
 
@@ -22,7 +22,7 @@ row4 a a id3
22
22
  tsv = TmpFile.with_file(content) do |filename|
23
23
  TSV.open(filename, :persist => false)
24
24
  end
25
-
25
+
26
26
  TmpFile.with_file(content2) do |filename|
27
27
  TSV.open(filename, :data => tsv)
28
28
  end
@@ -41,9 +41,14 @@ row2 a a id3
41
41
  EOF
42
42
 
43
43
  tsv = TmpFile.with_file(content) do |filename|
44
+ tsv = TSV.open(filename, :persist => true)
45
+ tsv.close
46
+ Persist::CONNECTIONS.clear
44
47
  TSV.open(filename, :persist => true)
45
48
  end
46
49
 
50
+ assert_equal "Id", tsv.key_field
51
+
47
52
  assert tsv.respond_to?(:persistence_class)
48
53
  assert_equal TokyoCabinet::HDB, tsv.persistence_class
49
54
 
@@ -61,7 +66,15 @@ row2 a a id3
61
66
  EOF
62
67
 
63
68
  tsv = TmpFile.with_file(content) do |filename|
64
- TSV.open(filename, :persist => true)
69
+ TSV.open(filename, :persist => false)
70
+ end
71
+
72
+ assert_include tsv.keys, 'row1'
73
+ assert_include tsv.keys, 'row2'
74
+ assert_equal %w(A a), tsv["row2"][0]
75
+
76
+ tsv = TmpFile.with_file(content) do |filename|
77
+ TSV.open(filename, :persist => true, :merge => true)
65
78
  end
66
79
 
67
80
  assert tsv.respond_to?(:persistence_class)
@@ -69,6 +82,212 @@ row2 a a id3
69
82
 
70
83
  assert_include tsv.keys, 'row1'
71
84
  assert_include tsv.keys, 'row2'
85
+ assert_equal %w(A a), tsv["row2"][0]
86
+ end
87
+
88
+ def test_headerless_fields
89
+ content =<<-EOF
90
+ row1 a|aa|aaa b Id1|Id2
91
+ row2 A B Id3
92
+ EOF
93
+
94
+ TmpFile.with_file(content) do |filename|
95
+ tsv = TSV.open(filename, :sep => /\s+/, :fields => [1])
96
+ assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
97
+ assert_equal :double, tsv.type
98
+ assert_equal [%w(a aa aaa)], tsv["row1"]
99
+ end
100
+ end
101
+
102
+ def test_tsv_field_selection
103
+ content =<<-EOF
104
+ #Id ValueA ValueB OtherID
105
+ row1 a|aa|aaa b Id1|Id2
106
+ row2 A B Id3
107
+ EOF
108
+
109
+ TmpFile.with_file(content) do |filename|
110
+ tsv = TSV.open(filename, :sep => /\s+/, :type => :single)
111
+ assert_equal ["ValueA"], tsv.fields
112
+ end
113
+ end
114
+
115
+ def test_tsv_single_from_flat
116
+ content =<<-EOF
117
+ #: :type=:flat
118
+ #Id Value
119
+ row1 1 2
120
+ row2 4
121
+ EOF
122
+
123
+ TmpFile.with_file(content) do |filename|
124
+ tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
125
+ assert_equal "row1", tsv["1"]
126
+ end
127
+ end
128
+
129
+ def test_key_field
130
+ content =<<-EOF
131
+ #: :sep=/\\s+/#:type=:single
132
+ #Id Value
133
+ a 1
134
+ b 2
135
+ EOF
136
+
137
+ TmpFile.with_file(content) do |filename|
138
+ tsv = TSV.open(filename, :key_field => "Value")
139
+ assert_equal %w(Id), tsv.fields
140
+ assert_equal "Value", tsv.key_field
141
+ assert_equal "a", tsv["1"]
142
+ end
143
+ end
144
+
145
+ def test_fix
146
+ content =<<-EOF
147
+ #: :sep=/\\s+/#:type=:single
148
+ #Id Value
149
+ a 1
150
+ b 2
151
+ EOF
152
+
153
+ TmpFile.with_file(content) do |filename|
154
+ tsv = TSV.open(filename, :key_field => "Value", :fix => Proc.new{|l| if l =~ /1/;then "a 3" else l end})
155
+ assert_equal "a", tsv["3"]
156
+ end
157
+ end
158
+
159
+ def test_flat
160
+ content =<<-EOF
161
+ #: :type=:flat
162
+ #Id Value
163
+ row1 a|aa|aaa
164
+ row2 A|AA|AAA
165
+ EOF
166
+
167
+ TmpFile.with_file(content) do |filename|
168
+ assert TSV.open(filename, :sep => /\s+/, :type => :flat).include? "row1"
169
+ assert TSV.open(filename, :sep => /\s+/, :type => :flat)["row1"].include? "a"
170
+ assert TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "Id")["row1"].include? "a"
171
+ assert TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "Id", :fields => ["Value"])["row1"].include? "a"
172
+ end
72
173
  end
73
- end
74
174
 
175
+ def test_tsv_flat_double
176
+ content =<<-EOF
177
+ #Id ValueA ValueB OtherID
178
+ row1 a|aa|aaa b Id1|Id2
179
+ row2 A B Id3
180
+ EOF
181
+
182
+ TmpFile.with_file(content) do |filename|
183
+ tsv = TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "ValueA", :fields => ["OtherID"], :merge => true)
184
+ assert tsv["aaa"].include? "Id1"
185
+ assert tsv["aaa"].include? "Id2"
186
+ end
187
+ end
188
+
189
+ def test_flat2single
190
+ content =<<-EOF
191
+ #: :type=:flat
192
+ #Id Value
193
+ row1 a aa aaa
194
+ row2 A AA AAA
195
+ EOF
196
+
197
+ TmpFile.with_file(content) do |filename|
198
+ tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value")
199
+ assert tsv.include? "aaa"
200
+ end
201
+ end
202
+
203
+ def test_flat_key
204
+ content =<<-EOF
205
+ #Id ValueA
206
+ row1 a aa aaa
207
+ row2 b bbb bbbb bb aa
208
+ EOF
209
+
210
+ TmpFile.with_file(content) do |filename|
211
+ tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :flat, :key_field => "ValueA")
212
+ assert_equal ["row1"], tsv["a"]
213
+ assert_equal ["row1", "row2"], tsv["aa"]
214
+ end
215
+ end
216
+
217
+ def test_unnamed_key
218
+ content =<<-EOF
219
+ row1 a|aa|aaa b Id1|Id2
220
+ row2 A B Id3
221
+ EOF
222
+
223
+ TmpFile.with_file(content) do |filename|
224
+ tsv = TSV.open(filename, :sep => /\s+/, :key_field => 1)
225
+ assert tsv.keys.include? "a"
226
+ end
227
+ end
228
+
229
+ def test_grep
230
+ content =<<-EOF
231
+ #: :sep=/\\s+/#:type=:single
232
+ #Id Value
233
+ a 1
234
+ b 2
235
+ c 3
236
+ EOF
237
+
238
+ TmpFile.with_file(content) do |filename|
239
+ tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
240
+ assert_includes tsv, "2"
241
+ refute_includes tsv, "3"
242
+ end
243
+ end
244
+
245
+ def TODO_test_tsv_grep
246
+ content =<<-EOF
247
+ #: :sep=/\\s+/#:type=:single
248
+ #Id Value
249
+ a 1
250
+ b 2
251
+ b 3
252
+ d 22
253
+ EOF
254
+
255
+ TmpFile.with_file(content) do |filename|
256
+ tsv = TSV.open(filename, :key_field => "Value", :tsv_grep => "2")
257
+ assert_includes tsv, "2"
258
+ refute_includes tsv, "3"
259
+ assert(tsv.include?("2"))
260
+ assert(! tsv.include?("3"))
261
+ end
262
+ end
263
+
264
+ def test_flat_with_field_header
265
+ content =<<-EOF
266
+ #: :type=:flat
267
+ #Id ValueA
268
+ row1 a aa aaa
269
+ row2 b bbb bbbb bb
270
+ EOF
271
+
272
+ TmpFile.with_file(content) do |filename|
273
+ tsv = TSV.open(filename, :sep => /\s+/, :merge => false)
274
+ assert_equal ["a", "aa", "aaa"], tsv["row1"]
275
+ end
276
+ end
277
+
278
+ def test_alt_args
279
+ content =<<-EOF
280
+ #Id ValueA
281
+ row1 a aa aaa
282
+ row2 b bbb bbbb bb
283
+ EOF
284
+
285
+ TmpFile.with_file(content) do |filename|
286
+ tsv = TSV.open(filename, type: :flat, :sep => /\s+/, :merge => false)
287
+ assert_equal ["a", "aa", "aaa"], tsv["row1"]
288
+ end
289
+
290
+ tsv = TSV.str_setup("ID~ValueA,ValueB#:type=:flat", {})
291
+ assert_equal "ID", tsv.key_field
292
+ end
293
+ end
@@ -103,18 +103,19 @@ class TestWorkQueue < Test::Unit::TestCase
103
103
  res << out
104
104
  end
105
105
 
106
- pid = Process.fork do
107
- reps.times do |i|
108
- q.write i
106
+ Log.with_severity 7 do
107
+ pid = Process.fork do
108
+ reps.times do |i|
109
+ q.write i
110
+ end
109
111
  end
110
- end
111
112
 
112
- Process.waitpid pid
113
- q.close
113
+ Process.waitpid pid
114
114
 
115
- assert_raise ScoutException do
116
- q.join
117
- t.join
115
+ assert_raise ScoutException do
116
+ q.join
117
+ t.join
118
+ end
118
119
  end
119
120
  end
120
121
 
@@ -128,20 +129,22 @@ class TestWorkQueue < Test::Unit::TestCase
128
129
 
129
130
  res = []
130
131
  q.process do |out|
131
- raise ScoutException if rand < 0.01
132
+ raise ScoutException
132
133
  res << out
133
134
  end
134
135
 
135
- pid = Process.fork do
136
- reps.times do |i|
137
- q.write i
136
+ Log.with_severity 7 do
137
+ pid = Process.fork do
138
+ reps.times do |i|
139
+ q.write i
140
+ end
141
+ q.close
138
142
  end
139
- q.close
140
- end
141
143
 
142
- assert_raise ScoutException do
143
- q.join
144
- t.join
144
+ assert_raise ScoutException do
145
+ q.join
146
+ t.join
147
+ end
145
148
  end
146
149
  end
147
150
  end
@@ -3,7 +3,7 @@ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1
3
3
 
4
4
  require 'scout/tsv'
5
5
  class TestTSVAdapter < Test::Unit::TestCase
6
- def test_get_set
6
+ def _test_get_set
7
7
  tsv = TSV.setup({}, :type => :list, :key_field => "Key", :fields => %w(one two three))
8
8
  tsv.type = :list
9
9
  tsv.extend TSVAdapter
@@ -30,5 +30,15 @@ class TestTSVAdapter < Test::Unit::TestCase
30
30
  assert_equal [["a", %w(1 2 3)], ["b", %w(11 22 33)]], tsv.sort
31
31
  assert_equal [["b", %w(11 22 33)], ["a", %w(1 2 3)]], tsv.sort_by{|k,v| -v[0].to_i }
32
32
  end
33
+
34
+ def test_serializer
35
+ tsv = TSV.setup({}, :type => :list, :key_field => "Key", :fields => %w(one two three))
36
+ tsv.type = :list
37
+ tsv.extend TSVAdapter
38
+ tsv.serializer = :integer_array
39
+ tsv["a"] = [1, 2, 3]
40
+
41
+ assert_equal [1, 2, 3], tsv["a"]
42
+ end
33
43
  end
34
44
 
@@ -0,0 +1,134 @@
1
+ require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
2
+ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
3
+
4
+ require 'scout/tsv'
5
+ class TestFixWidthTable < Test::Unit::TestCase
6
+ def load_data(data)
7
+ tsv = TSV.open(data, type: :list, :sep=>":", :cast => proc{|e| e =~ /(\s*)(_*)/; ($1.length..($1.length + $2.length - 1))})
8
+ tsv.add_field "Start" do |key, values|
9
+ values["Range"].first
10
+ end
11
+ tsv.add_field "End" do |key, values|
12
+ values["Range"].last
13
+ end
14
+
15
+ tsv = tsv.slice ["Start", "End"]
16
+
17
+ tsv
18
+ end
19
+
20
+ def test_options
21
+ TmpFile.with_file do |filename|
22
+ f = FixWidthTable.new filename, 100, true
23
+ f.close
24
+
25
+ f1 = FixWidthTable.new filename, 100, false
26
+
27
+ assert_equal true, f1.range
28
+ end
29
+ end
30
+
31
+ def test_add
32
+ TmpFile.with_file do |filename|
33
+ f = FixWidthTable.new filename, 100, true
34
+ f.add [1,2,0], "test1"
35
+ f.add [3,4,0], "test2"
36
+ f.read
37
+
38
+ assert_equal 1, f.idx_pos(0)
39
+ assert_equal 3, f.idx_pos(1)
40
+ assert_equal 2, f.idx_pos_end(0)
41
+ assert_equal 4, f.idx_pos_end(1)
42
+ assert_equal 0, f.idx_overlap(0)
43
+ assert_equal 0, f.idx_overlap(1)
44
+ assert_equal "test1", f.idx_value(0)
45
+ assert_equal "test2", f.idx_value(1)
46
+
47
+ end
48
+
49
+ end
50
+
51
+ def test_point
52
+ data =<<-EOF
53
+ #: :sep=/\\s+/#:type=:single#:cast=:to_i
54
+ #ID Pos
55
+ a 1
56
+ b 10
57
+ c 20
58
+ d 12
59
+ e 26
60
+ f 11
61
+ g 25
62
+ EOF
63
+ TmpFile.with_file(data) do |datafile|
64
+ tsv = TSV.open datafile
65
+ TmpFile.with_file do |filename|
66
+ f = FixWidthTable.new filename, 100, false
67
+ f.add_point tsv
68
+ f.read
69
+
70
+ assert_equal %w(), f[0].sort
71
+ assert_equal %w(b), f[10].sort
72
+ assert_equal %w(a b c d f), f[(0..20)].sort
73
+ end
74
+ end
75
+ end
76
+
77
+ def test_range
78
+ data =<<-EOF
79
+ ##012345678901234567890
80
+ #ID:Range
81
+ a: ______
82
+ b: ______
83
+ c: _______
84
+ d: ____
85
+ e: ______
86
+ f: ___
87
+ g: ____
88
+ EOF
89
+ TmpFile.with_file(data) do |datafile|
90
+ tsv = load_data(datafile)
91
+ TmpFile.with_file do |filename|
92
+ f = FixWidthTable.new filename, 100, true
93
+ f.add_range tsv
94
+ f.read
95
+
96
+ assert_equal %w(), f[0].sort
97
+ assert_equal %w(b), f[1].sort
98
+ assert_equal %w(), f[20].sort
99
+ assert_equal %w(), f[(20..100)].sort
100
+ assert_equal %w(a b d), f[3].sort
101
+ assert_equal %w(a b c d e), f[(3..4)].sort
102
+ assert_equal %w(a c e), f[7].sort
103
+ end
104
+ end
105
+ end
106
+
107
+
108
+ def test_range_pos
109
+ data =<<-EOF
110
+ ##012345678901234567890
111
+ #ID:Range
112
+ a: ______
113
+ b: ______
114
+ c: _______
115
+ d: ____
116
+ e: ______
117
+ f: ___
118
+ g: ____
119
+ EOF
120
+ TmpFile.with_file(data) do |datafile|
121
+ tsv = load_data(datafile)
122
+ TmpFile.with_file do |filename|
123
+ f = FixWidthTable.new filename, 100, true
124
+ f.add_range tsv
125
+ f.read
126
+
127
+ assert_equal %w(), f.overlaps(0).sort
128
+ assert_equal %w(1:6), f.overlaps(1).sort
129
+ assert_equal %w(1:6:b), f.overlaps(1, true).sort
130
+ end
131
+ end
132
+ end
133
+ end
134
+
@@ -21,6 +21,11 @@ row2 a a id3
21
21
 
22
22
  assert_equal %w(a aa aaa), tsv["row1"][0]
23
23
 
24
+ assert TSVAdapter === tsv
25
+ assert TSV === tsv
26
+ assert_include tsv.instance_variable_get(:@extension_attrs), :key_field
27
+ assert_include tsv.instance_variable_get(:@extension_attrs), :serializer
28
+
24
29
  tsv_loaded = assert_nothing_raised do
25
30
  TmpFile.with_file(content) do |filename|
26
31
  Persist.persist(__method__, :HDB) do
@@ -29,6 +34,7 @@ row2 a a id3
29
34
  end
30
35
  end
31
36
 
37
+
32
38
  assert_equal %w(a aa aaa), tsv_loaded["row1"][0]
33
39
  end
34
40
 
@@ -54,7 +60,7 @@ row2 a a id3
54
60
  end
55
61
  end
56
62
 
57
- def test_speed
63
+ def __test_speed
58
64
  tsv = TSV.setup({}, :type => :double, :key_field => "Key", :fields => %w(Field1 Field2))
59
65
 
60
66
  size = 100_000
@@ -88,5 +94,27 @@ row2 a a id3
88
94
  assert_equal tc["key-#{i}"], tsv["key-#{i}"]
89
95
  end
90
96
  end
97
+
98
+ def test_float_array
99
+ content =<<-EOF
100
+ #Id ValueA ValueB OtherID
101
+ row1 0.2 0.3 0
102
+ row2 0.1 4.5 0
103
+ EOF
104
+
105
+ TmpFile.with_file(content) do |filename|
106
+ tsv = TSV.open(filename, :sep => /\s+/, :persist => true, :type => :list, :cast => :to_f)
107
+ tsv.save_extension_attr_hash
108
+ assert_equal [0.2, 0.3, 0], tsv["row1"]
109
+ assert_equal TSVAdapter::FloatArraySerializer, tsv.serializer
110
+ Open.cp tsv.persistence_path, tmpdir.persistence.foo
111
+ tsv2 = ScoutCabinet.open(tmpdir.persistence.foo, false)
112
+ tsv2.extend TSVAdapter
113
+ assert_equal [0.2, 0.3, 0], tsv2["row1"]
114
+ assert_equal TSVAdapter::FloatArraySerializer, tsv2.serializer
115
+ end
116
+
117
+ end
118
+
91
119
  end
92
120