optimus-ep 0.10.3 → 0.10.4
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- checksums.yaml +7 -0
- data/.gitignore +18 -0
- data/CHANGELOG +2 -0
- data/Gemfile +4 -0
- data/lib/optimus_reader.rb +16 -12
- data/lib/tabfile_parser.rb +16 -3
- data/lib/version.rb +2 -7
- data/optimus-ep.gemspec +19 -32
- data/spec/samples/.gitattributes +1 -0
- metadata +56 -59
- data/autotest/discover.rb +0 -1
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: 9c5410cc89e909a9dd6b0cb2bdea464d4857de53
|
4
|
+
data.tar.gz: 42c34c6d72a81c67bfe9fa8cb66543e9131bb21a
|
5
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+
SHA512:
|
6
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+
metadata.gz: 1d25abe2d6a0fdcb90ffb143c5634dd220abc0b977dfd515228237f127d0c9e59b8376e5349052bbd66927b4e33db2be224de454158caeb573d6a28b82f1c279
|
7
|
+
data.tar.gz: c546b812bce35c5ad96bca18c0db1803582b69228327279b993a312b7f5c1c723c75ae2d6cc14e252793f2d8dd096fe1c799eff8eadce69b4b871b2e9d86d746
|
data/.gitignore
ADDED
data/CHANGELOG
CHANGED
data/Gemfile
ADDED
data/lib/optimus_reader.rb
CHANGED
@@ -60,18 +60,19 @@ module Optimus
|
|
60
60
|
converted_f = nil
|
61
61
|
file.rewind
|
62
62
|
datas = file.read(2)
|
63
|
-
if datas
|
63
|
+
if datas.respond_to? :encode and
|
64
|
+
datas == "\xff\xfe".force_encoding("ASCII-8BIT")
|
65
|
+
# Ruby 1.9.x -- iconv is deprecated here
|
64
66
|
file_data = file.read
|
65
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-
|
66
|
-
|
67
|
-
|
68
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-
|
69
|
-
|
70
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-
|
71
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-
|
72
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-
|
73
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-
|
74
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-
end
|
67
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+
converted_f = StringIO.new(
|
68
|
+
file_data.encode("UTF-8", "UTF-16LE"))
|
69
|
+
elsif not datas.respond_to? :encode and
|
70
|
+
datas == "\xff\xfe"
|
71
|
+
# Ruby 1.8.x -- no String#encode()
|
72
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+
file_data = file.read
|
73
|
+
require 'iconv'
|
74
|
+
converted_f = StringIO.new(
|
75
|
+
Iconv.conv("UTF-8", "UTF-16LE", file_data))
|
75
76
|
else
|
76
77
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converted_f = file
|
77
78
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converted_f.rewind
|
@@ -91,6 +92,9 @@ module Optimus
|
|
91
92
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2.times do
|
92
93
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first_lines << @file.gets
|
93
94
|
end
|
95
|
+
unless first_lines[1]
|
96
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+
first_lines = first_lines[0].gsub(/\r\n?/, '\n').split('\n')[0..1]
|
97
|
+
end
|
94
98
|
@file.pos = original_pos
|
95
99
|
@type = determine_file_type(first_lines)
|
96
100
|
if @type.nil?
|
@@ -115,4 +119,4 @@ module Optimus
|
|
115
119
|
}
|
116
120
|
end
|
117
121
|
end
|
118
|
-
end
|
122
|
+
end
|
data/lib/tabfile_parser.rb
CHANGED
@@ -24,15 +24,28 @@ module Optimus
|
|
24
24
|
@file = file
|
25
25
|
@skip_lines = options[:skip_lines] || 0
|
26
26
|
@columns = options[:columns]
|
27
|
+
@merge_header_lines = options[:merge_header_lines] || 1
|
27
28
|
end
|
28
29
|
|
29
30
|
def to_optimus
|
30
|
-
lines = @file.
|
31
|
+
lines = @file.read
|
32
|
+
lines.gsub!(/\r\n?/,"\n")
|
33
|
+
lines = lines.split("\n")
|
34
|
+
|
35
|
+
raise DamagedFileError.new("File #{@file.path} appears to be empty.") if lines.nil?
|
36
|
+
|
31
37
|
@skip_lines.times do
|
32
38
|
lines.shift
|
33
39
|
end
|
34
40
|
|
35
|
-
|
41
|
+
headers = []
|
42
|
+
|
43
|
+
@merge_header_lines.times do
|
44
|
+
l = lines.shift
|
45
|
+
headers << l.split("\t",-1).map {|elt| elt.strip }
|
46
|
+
end
|
47
|
+
file_columns = headers[0].zip(*headers[1..-1]).map{|labels| labels.join(' ')}
|
48
|
+
|
36
49
|
expected_size = file_columns.size
|
37
50
|
columns = file_columns
|
38
51
|
data = Optimus::Data.new(columns)
|
@@ -40,7 +53,7 @@ module Optimus
|
|
40
53
|
lines.each do |line|
|
41
54
|
current_line += 1
|
42
55
|
row = data.add_row
|
43
|
-
col_data = line.split("\t").map {|e| e.strip }
|
56
|
+
col_data = line.split("\t",-1).map {|e| e.strip }
|
44
57
|
if col_data.size != expected_size
|
45
58
|
raise DamagedFileError.new("In #{@file.path}, line #{current_line} should have #{expected_size} columns but had #{col_data.size}.")
|
46
59
|
end
|
data/lib/version.rb
CHANGED
data/optimus-ep.gemspec
CHANGED
@@ -1,36 +1,23 @@
|
|
1
1
|
# -*- encoding: utf-8 -*-
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'version'
|
2
5
|
|
3
|
-
Gem::Specification.new do |
|
4
|
-
|
5
|
-
|
6
|
+
Gem::Specification.new do |gem|
|
7
|
+
gem.name = "optimus-ep"
|
8
|
+
gem.version = Optimus::VERSION
|
9
|
+
gem.authors = ["Nate Vack"]
|
10
|
+
gem.email = ["njvack@wisc.edu"]
|
11
|
+
gem.description = %q{Utilities to process behavioral data generated by E-Prime}
|
12
|
+
gem.summary = %q{Utilities to process behavioral data generated by E-Prime}
|
13
|
+
gem.homepage = "http://github.com/njvack/optimus-ep"
|
6
14
|
|
7
|
-
|
8
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-
|
9
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-
|
10
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-
|
11
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-
|
12
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-
|
13
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-
|
14
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-
|
15
|
-
s.homepage = "http://github.com/njvack/optimus-ep"
|
16
|
-
s.rdoc_options = ["--line-numbers", "--inline-source", "--title", "Optimus-ep", "--main", "README"]
|
17
|
-
s.require_paths = ["lib"]
|
18
|
-
s.rubyforge_project = "optimus-ep"
|
19
|
-
s.rubygems_version = "1.8.23"
|
20
|
-
s.summary = "Utilities to process behavioral data generated by E-Prime"
|
21
|
-
|
22
|
-
if s.respond_to? :specification_version then
|
23
|
-
s.specification_version = 3
|
24
|
-
|
25
|
-
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
26
|
-
s.add_runtime_dependency(%q<rparsec-ruby19>, [">= 1.0"])
|
27
|
-
s.add_development_dependency(%q<rspec>, [">= 0"])
|
28
|
-
else
|
29
|
-
s.add_dependency(%q<rparsec-ruby19>, [">= 1.0"])
|
30
|
-
s.add_dependency(%q<rspec>, [">= 0"])
|
31
|
-
end
|
32
|
-
else
|
33
|
-
s.add_dependency(%q<rparsec-ruby19>, [">= 1.0"])
|
34
|
-
s.add_dependency(%q<rspec>, [">= 0"])
|
35
|
-
end
|
15
|
+
gem.files = `git ls-files`.split($/)
|
16
|
+
gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
|
17
|
+
gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
|
18
|
+
gem.require_paths = ["lib"]
|
19
|
+
|
20
|
+
gem.add_runtime_dependency "rparsec-ruby19", ">=1.0"
|
21
|
+
gem.add_development_dependency "rspec"
|
22
|
+
|
36
23
|
end
|
@@ -0,0 +1 @@
|
|
1
|
+
* -text
|
metadata
CHANGED
@@ -1,92 +1,61 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: optimus-ep
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.10.
|
5
|
-
prerelease:
|
4
|
+
version: 0.10.4
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
7
|
- Nate Vack
|
9
8
|
autorequire:
|
10
9
|
bindir: bin
|
11
10
|
cert_chain: []
|
12
|
-
date:
|
11
|
+
date: 2015-07-14 00:00:00.000000000 Z
|
13
12
|
dependencies:
|
14
13
|
- !ruby/object:Gem::Dependency
|
15
14
|
name: rparsec-ruby19
|
16
15
|
requirement: !ruby/object:Gem::Requirement
|
17
|
-
none: false
|
18
16
|
requirements:
|
19
|
-
- -
|
17
|
+
- - ">="
|
20
18
|
- !ruby/object:Gem::Version
|
21
19
|
version: '1.0'
|
22
20
|
type: :runtime
|
23
21
|
prerelease: false
|
24
22
|
version_requirements: !ruby/object:Gem::Requirement
|
25
|
-
none: false
|
26
23
|
requirements:
|
27
|
-
- -
|
24
|
+
- - ">="
|
28
25
|
- !ruby/object:Gem::Version
|
29
26
|
version: '1.0'
|
30
27
|
- !ruby/object:Gem::Dependency
|
31
28
|
name: rspec
|
32
29
|
requirement: !ruby/object:Gem::Requirement
|
33
|
-
none: false
|
34
30
|
requirements:
|
35
|
-
- -
|
31
|
+
- - ">="
|
36
32
|
- !ruby/object:Gem::Version
|
37
33
|
version: '0'
|
38
34
|
type: :development
|
39
35
|
prerelease: false
|
40
36
|
version_requirements: !ruby/object:Gem::Requirement
|
41
|
-
none: false
|
42
37
|
requirements:
|
43
|
-
- -
|
38
|
+
- - ">="
|
44
39
|
- !ruby/object:Gem::Version
|
45
40
|
version: '0'
|
46
41
|
description: Utilities to process behavioral data generated by E-Prime
|
47
|
-
email:
|
42
|
+
email:
|
43
|
+
- njvack@wisc.edu
|
48
44
|
executables:
|
49
45
|
- eprime2tabfile
|
50
46
|
- extract_timings
|
51
47
|
extensions: []
|
52
|
-
extra_rdoc_files:
|
53
|
-
- CHANGELOG
|
54
|
-
- LICENSE
|
55
|
-
- README
|
56
|
-
- README.textile
|
57
|
-
- bin/eprime2tabfile
|
58
|
-
- bin/extract_timings
|
59
|
-
- lib/eprimetab_parser.rb
|
60
|
-
- lib/excel_parser.rb
|
61
|
-
- lib/expression_parser/evaluators.rb
|
62
|
-
- lib/expression_parser/expressions.rb
|
63
|
-
- lib/log_file_parser.rb
|
64
|
-
- lib/optimus.rb
|
65
|
-
- lib/optimus_data.rb
|
66
|
-
- lib/optimus_reader.rb
|
67
|
-
- lib/parsed_calculator.rb
|
68
|
-
- lib/raw_tab_parser.rb
|
69
|
-
- lib/runners/generic_runner.rb
|
70
|
-
- lib/runners/yaml_template/option_parser.rb
|
71
|
-
- lib/runners/yaml_template/runner.rb
|
72
|
-
- lib/tabfile_parser.rb
|
73
|
-
- lib/tabfile_writer.rb
|
74
|
-
- lib/transformers/basic_transformer.rb
|
75
|
-
- lib/transformers/column_calculator.rb
|
76
|
-
- lib/transformers/multipasser.rb
|
77
|
-
- lib/transformers/row_filter.rb
|
78
|
-
- lib/transformers/timing_extractor.rb
|
79
|
-
- lib/version.rb
|
80
|
-
- lib/writers/stimtimes_writer.rb
|
48
|
+
extra_rdoc_files: []
|
81
49
|
files:
|
50
|
+
- ".gitignore"
|
82
51
|
- CHANGELOG
|
83
52
|
- GPL.txt
|
53
|
+
- Gemfile
|
84
54
|
- LICENSE
|
85
55
|
- Manifest
|
86
56
|
- README
|
87
57
|
- README.textile
|
88
58
|
- Rakefile
|
89
|
-
- autotest/discover.rb
|
90
59
|
- bin/eprime2tabfile
|
91
60
|
- bin/extract_timings
|
92
61
|
- lib/eprimetab_parser.rb
|
@@ -111,6 +80,7 @@ files:
|
|
111
80
|
- lib/transformers/timing_extractor.rb
|
112
81
|
- lib/version.rb
|
113
82
|
- lib/writers/stimtimes_writer.rb
|
83
|
+
- optimus-ep.gemspec
|
114
84
|
- spec/eprimetab_parser_spec.rb
|
115
85
|
- spec/excel_parser_spec.rb
|
116
86
|
- spec/expression_parser/evaluators_spec.rb
|
@@ -123,6 +93,7 @@ files:
|
|
123
93
|
- spec/runners/generic_runner_spec.rb
|
124
94
|
- spec/runners/yaml_template/option_parser_spec.rb
|
125
95
|
- spec/runners/yaml_template/runner_spec.rb
|
96
|
+
- spec/samples/.gitattributes
|
126
97
|
- spec/samples/bad_excel_tsv.txt
|
127
98
|
- spec/samples/corrupt_log_file.txt
|
128
99
|
- spec/samples/eprime_tsv.txt
|
@@ -144,35 +115,61 @@ files:
|
|
144
115
|
- spec/transformers/row_filter_spec.rb
|
145
116
|
- spec/transformers/timing_extractor_spec.rb
|
146
117
|
- spec/writers/stimtimes_writer_spec.rb
|
147
|
-
- optimus-ep.gemspec
|
148
118
|
homepage: http://github.com/njvack/optimus-ep
|
149
119
|
licenses: []
|
120
|
+
metadata: {}
|
150
121
|
post_install_message:
|
151
|
-
rdoc_options:
|
152
|
-
- --line-numbers
|
153
|
-
- --inline-source
|
154
|
-
- --title
|
155
|
-
- Optimus-ep
|
156
|
-
- --main
|
157
|
-
- README
|
122
|
+
rdoc_options: []
|
158
123
|
require_paths:
|
159
124
|
- lib
|
160
125
|
required_ruby_version: !ruby/object:Gem::Requirement
|
161
|
-
none: false
|
162
126
|
requirements:
|
163
|
-
- -
|
127
|
+
- - ">="
|
164
128
|
- !ruby/object:Gem::Version
|
165
129
|
version: '0'
|
166
130
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
167
|
-
none: false
|
168
131
|
requirements:
|
169
|
-
- -
|
132
|
+
- - ">="
|
170
133
|
- !ruby/object:Gem::Version
|
171
|
-
version: '
|
134
|
+
version: '0'
|
172
135
|
requirements: []
|
173
|
-
rubyforge_project:
|
174
|
-
rubygems_version:
|
136
|
+
rubyforge_project:
|
137
|
+
rubygems_version: 2.2.2
|
175
138
|
signing_key:
|
176
|
-
specification_version:
|
139
|
+
specification_version: 4
|
177
140
|
summary: Utilities to process behavioral data generated by E-Prime
|
178
|
-
test_files:
|
141
|
+
test_files:
|
142
|
+
- spec/eprimetab_parser_spec.rb
|
143
|
+
- spec/excel_parser_spec.rb
|
144
|
+
- spec/expression_parser/evaluators_spec.rb
|
145
|
+
- spec/expression_parser/expressions_spec.rb
|
146
|
+
- spec/log_file_parser_spec.rb
|
147
|
+
- spec/optimus_data_spec.rb
|
148
|
+
- spec/optimus_reader_spec.rb
|
149
|
+
- spec/parsed_calculator_spec.rb
|
150
|
+
- spec/raw_tab_parser_spec.rb
|
151
|
+
- spec/runners/generic_runner_spec.rb
|
152
|
+
- spec/runners/yaml_template/option_parser_spec.rb
|
153
|
+
- spec/runners/yaml_template/runner_spec.rb
|
154
|
+
- spec/samples/.gitattributes
|
155
|
+
- spec/samples/bad_excel_tsv.txt
|
156
|
+
- spec/samples/corrupt_log_file.txt
|
157
|
+
- spec/samples/eprime_tsv.txt
|
158
|
+
- spec/samples/excel_tsv.txt
|
159
|
+
- spec/samples/optimus_log.txt
|
160
|
+
- spec/samples/optimus_log_utf16le.txt
|
161
|
+
- spec/samples/raw_tsv.txt
|
162
|
+
- spec/samples/short_columns.txt
|
163
|
+
- spec/samples/sorted_columns.txt
|
164
|
+
- spec/samples/std_columns.txt
|
165
|
+
- spec/samples/unknown_type.txt
|
166
|
+
- spec/samples/unreadable_file
|
167
|
+
- spec/spec_helper.rb
|
168
|
+
- spec/tabfile_parser_spec.rb
|
169
|
+
- spec/tabfile_writer_spec.rb
|
170
|
+
- spec/transformers/basic_transformer_spec.rb
|
171
|
+
- spec/transformers/column_calculator_spec.rb
|
172
|
+
- spec/transformers/multipasser_spec.rb
|
173
|
+
- spec/transformers/row_filter_spec.rb
|
174
|
+
- spec/transformers/timing_extractor_spec.rb
|
175
|
+
- spec/writers/stimtimes_writer_spec.rb
|
data/autotest/discover.rb
DELETED
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Autotest.add_discovery { "rspec2" }
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