answer-factory 0.1.2 → 0.1.3.4
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- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/answer-factory.gemspec +15 -8
- data/lib/answer-factory.rb +2 -0
- data/lib/factories/factory.rb +7 -0
- data/lib/factories/workstation.rb +16 -0
- data/lib/machines/evaluate_with_test_cases.rb +140 -0
- data/lib/machines/infrastructure.rb +2 -0
- data/lib/machines/select_by_summed_rank.rb +54 -0
- data/spec/factories/factory_spec.rb +13 -1
- data/spec/factories/workstation_spec.rb +19 -0
- data/spec/fixtures/my_data_source.csv +4 -0
- data/spec/integration_specs/couch_db_integration.rspec +59 -1
- data/spec/machines/evaluate_with_test_cases_spec.rb +296 -0
- data/spec/machines/select_by_summed_rank_spec.rb +134 -0
- data/spec/machines/select_nondominated_spec.rb +8 -0
- data/spec/spec_helper.rb +2 -1
- data/templates/answer_factory_activate_template.erb +44 -56
- metadata +33 -5
data/Rakefile
CHANGED
@@ -12,7 +12,7 @@ begin
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12
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gemspec.required_ruby_version = '>= 1.9.1'
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15
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-
gemspec.add_dependency('nudge', '>= 0.2')
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15
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+
gemspec.add_dependency('nudge', '>= 0.2.9')
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gemspec.add_dependency('thor', '>= 0.13')
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gemspec.add_dependency('couchrest', '>= 0.33')
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gemspec.add_dependency('configatron', '>= 2.6.2')
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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1
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+
0.1.3.4
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data/answer-factory.gemspec
CHANGED
@@ -1,15 +1,15 @@
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1
1
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# Generated by jeweler
|
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2
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# DO NOT EDIT THIS FILE DIRECTLY
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-
# Instead, edit Jeweler::Tasks in
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3
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+
# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
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4
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# -*- encoding: utf-8 -*-
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5
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Gem::Specification.new do |s|
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s.name = %q{answer-factory}
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8
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-
s.version = "0.1.
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8
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+
s.version = "0.1.3.4"
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9
9
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10
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Bill Tozier", "Trek Glowacki", "Jesse Sielaff"]
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-
s.date = %q{2010-05-
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12
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+
s.date = %q{2010-05-27}
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s.default_executable = %q{answer-factory}
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s.description = %q{The pragmaticgp gem provides a simple framework for building, running and managing genetic programming experiments which automatically discover algorithms and equations to solve user-defined problems.}
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s.email = %q{bill@vagueinnovation.com}
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@@ -34,20 +34,25 @@ Gem::Specification.new do |s|
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"lib/machines/any_one.rb",
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"lib/machines/build_random.rb",
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"lib/machines/evaluate_simple_score.rb",
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+
"lib/machines/evaluate_with_test_cases.rb",
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"lib/machines/infrastructure.rb",
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"lib/machines/mutate_footnotes.rb",
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40
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+
"lib/machines/select_by_summed_rank.rb",
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"lib/machines/select_nondominated.rb",
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"readme.md",
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"spec/answers/answer_spec.rb",
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"spec/answers/batch_spec.rb",
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"spec/factories/factory_spec.rb",
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"spec/factories/workstation_spec.rb",
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+
"spec/fixtures/my_data_source.csv",
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"spec/integration_specs/couch_db_integration.rspec",
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"spec/machines/any_one_spec.rb",
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"spec/machines/build_random_spec.rb",
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"spec/machines/evaluate_simple_score_spec.rb",
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+
"spec/machines/evaluate_with_test_cases_spec.rb",
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"spec/machines/infrastructure_spec.rb",
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"spec/machines/mutate_footnotes_spec.rb",
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+
"spec/machines/select_by_summed_rank_spec.rb",
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"spec/machines/select_nondominated_spec.rb",
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"spec/spec_helper.rb",
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"tasks/setup_factory.thor",
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@@ -58,7 +63,7 @@ Gem::Specification.new do |s|
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s.rdoc_options = ["--charset=UTF-8"]
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s.require_paths = ["lib"]
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s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
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-
s.rubygems_version = %q{1.3.
|
66
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+
s.rubygems_version = %q{1.3.7}
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s.summary = %q{Genetic Programming in the Nudge language}
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s.test_files = [
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"spec/answers/answer_spec.rb",
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@@ -68,8 +73,10 @@ Gem::Specification.new do |s|
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"spec/machines/any_one_spec.rb",
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"spec/machines/build_random_spec.rb",
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"spec/machines/evaluate_simple_score_spec.rb",
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+
"spec/machines/evaluate_with_test_cases_spec.rb",
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"spec/machines/infrastructure_spec.rb",
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"spec/machines/mutate_footnotes_spec.rb",
|
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+
"spec/machines/select_by_summed_rank_spec.rb",
|
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"spec/machines/select_nondominated_spec.rb",
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"spec/spec_helper.rb"
|
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]
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@@ -78,8 +85,8 @@ Gem::Specification.new do |s|
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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s.specification_version = 3
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87
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81
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-
if Gem::Version.new(Gem::
|
82
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-
s.add_runtime_dependency(%q<nudge>, [">= 0.2"])
|
88
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+
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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89
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+
s.add_runtime_dependency(%q<nudge>, [">= 0.2.9"])
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90
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s.add_runtime_dependency(%q<thor>, [">= 0.13"])
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s.add_runtime_dependency(%q<couchrest>, [">= 0.33"])
|
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s.add_runtime_dependency(%q<configatron>, [">= 2.6.2"])
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@@ -87,7 +94,7 @@ Gem::Specification.new do |s|
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87
94
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s.add_runtime_dependency(%q<sinatra>, [">= 0.9.4"])
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s.add_runtime_dependency(%q<activesupport>, [">= 2.3.5"])
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else
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-
s.add_dependency(%q<nudge>, [">= 0.2"])
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+
s.add_dependency(%q<nudge>, [">= 0.2.9"])
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s.add_dependency(%q<thor>, [">= 0.13"])
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s.add_dependency(%q<couchrest>, [">= 0.33"])
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s.add_dependency(%q<configatron>, [">= 2.6.2"])
|
@@ -96,7 +103,7 @@ Gem::Specification.new do |s|
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96
103
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s.add_dependency(%q<activesupport>, [">= 2.3.5"])
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end
|
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105
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else
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99
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-
s.add_dependency(%q<nudge>, [">= 0.2"])
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+
s.add_dependency(%q<nudge>, [">= 0.2.9"])
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s.add_dependency(%q<thor>, [">= 0.13"])
|
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108
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s.add_dependency(%q<couchrest>, [">= 0.33"])
|
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109
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s.add_dependency(%q<configatron>, [">= 2.6.2"])
|
data/lib/answer-factory.rb
CHANGED
@@ -13,7 +13,9 @@ require 'machines/infrastructure'
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|
13
13
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require 'machines/any_one'
|
14
14
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require 'machines/build_random'
|
15
15
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require 'machines/evaluate_simple_score'
|
16
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+
require 'machines/evaluate_with_test_cases'
|
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17
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require 'machines/select_nondominated'
|
18
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+
require 'machines/select_by_summed_rank'
|
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19
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require 'machines/mutate_footnotes'
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18
20
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19
21
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data/lib/factories/factory.rb
CHANGED
@@ -26,6 +26,8 @@ module AnswerFactory
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26
26
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@couchdb_server = options[:couchdb_server] ||
|
27
27
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configatron.factory.couchdb.retrieve(:server, nil) ||
|
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"http://127.0.0.1:5984"
|
29
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+
|
30
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+
|
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|
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@couchdb_name = options[:couchdb_name] ||
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configatron.factory.couchdb.retrieve(:name, nil) ||
|
@@ -54,6 +56,7 @@ module AnswerFactory
|
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54
56
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configatron.factory.workstation_names = @workstation_names
|
55
57
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configatron.factory.couchdb.server = @couchdb_server
|
56
58
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configatron.factory.couchdb.name = @couchdb_name
|
59
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+
configatron.factory.training_datasource = self.training_datasource
|
57
60
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end
|
58
61
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|
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@@ -63,5 +66,9 @@ module AnswerFactory
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63
66
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rescue StandardError
|
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false
|
65
68
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end
|
69
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+
|
70
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+
def training_datasource
|
71
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"#{@couchdb_server}/#{@name}_training"
|
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+
end
|
66
73
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end
|
67
74
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end
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@@ -52,6 +52,22 @@ module AnswerFactory
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52
52
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end
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53
53
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54
54
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55
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+
def couchdb_viewdoc
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56
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{'_id' => "_design/#{@name.to_s}",
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views: {
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current: {
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map: "function(doc) { if(doc.location == '#{@name.to_s}') { emit(doc._id, doc); } }"
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+
}
|
61
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+
}
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}
|
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end
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64
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+
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65
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+
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66
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+
def couchdb_create_view(db_uri = couchdb_uri)
|
67
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+
CouchRest.database!(db_uri).save_doc(self.couchdb_viewdoc, use_uuids=false)
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+
end
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+
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70
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+
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def ship!
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# Workstation is a superclass; the default behavior (doing nothing)
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# should be overridden in a subclass definition
|
@@ -0,0 +1,140 @@
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1
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#encoding: utf-8
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module AnswerFactory
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module Machines
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4
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+
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5
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+
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6
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class EvaluateWithTestCases < Machine
|
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attr_accessor :sensors
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attr_accessor :test_cases
|
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attr_reader :name
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attr_reader :csv_filename
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+
|
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def initialize(options = {})
|
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super
|
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@name = options[:name] || "evaluator"
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@sensors = options[:sensors] || {}
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@csv_filename = options[:training_data_csv]
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self.load_training_data!
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end
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def score(batch, overridden_options = {})
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all_options = @options.merge(overridden_options)
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name = all_options[:name]
|
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+
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26
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+
|
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+
raise ArgumentError, "EvaluateWithTestCases#score cannot process a #{batch.class}" unless
|
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+
batch.kind_of?(Batch)
|
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+
raise ArgumentError, "EvaluateWithTestCases: Undefined #name attribute" if
|
30
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+
name.nil?
|
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+
|
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+
load_training_data!
|
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+
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batch.each do |answer|
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raw_results = Hash.new {|hash, key| hash[key] = []}
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+
|
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@test_cases.each do |t|
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+
|
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interpreter = Interpreter.new(answer.blueprint,all_options)
|
41
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+
|
42
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+
t.inputs.each do |variable_header, variable_value|
|
43
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+
variable_name, variable_type = variable_header.split(":")
|
44
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+
interpreter.bind_variable(variable_name, ValuePoint.new(variable_type, variable_value))
|
45
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+
end
|
46
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+
|
47
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+
@sensors.each do |sensor_name, sensor_block|
|
48
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+
interpreter.register_sensor(sensor_name, &sensor_block)
|
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+
end
|
50
|
+
|
51
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+
interpreter.run.each do |sensor_name, sensor_result|
|
52
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+
raw_results[sensor_name] << (t.outputs[sensor_name].to_i - sensor_result)
|
53
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+
end
|
54
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+
end
|
55
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+
|
56
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+
@sensors.each do |sensor_name, sensor_block|
|
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+
answer.scores[sensor_name] = raw_results[sensor_name].inject(0) do |sum, measurement|
|
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+
sum + measurement.abs
|
59
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+
end
|
60
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+
end
|
61
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+
end
|
62
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+
|
63
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+
|
64
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+
return batch
|
65
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+
end
|
66
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+
|
67
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+
|
68
|
+
def training_datasource
|
69
|
+
configatron.factory.training_datasource
|
70
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+
end
|
71
|
+
|
72
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+
|
73
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+
def training_data_view
|
74
|
+
"#{configatron.factory.training_datasource}/_design/#{@name}/_view/test_cases"
|
75
|
+
end
|
76
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+
|
77
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+
|
78
|
+
def header_prep(header_string)
|
79
|
+
raise ArgumentError, "Header must match /reference_name:nudge_type/" unless
|
80
|
+
header_string.match /[\p{Alpha}][\p{Alnum}_]*:[\p{Alpha}][\p{Alnum}_]/
|
81
|
+
header_string.strip
|
82
|
+
end
|
83
|
+
|
84
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+
|
85
|
+
def build_sensor(name, &block)
|
86
|
+
@sensors[name] = block
|
87
|
+
end
|
88
|
+
|
89
|
+
|
90
|
+
def install_training_data_from_csv(csv_filename = @csv_filename)
|
91
|
+
reader = CSV.new(File.open(csv_filename), headers: true)
|
92
|
+
reader.readline
|
93
|
+
split_point = reader.headers.find_index(nil)
|
94
|
+
|
95
|
+
input_headers = reader.headers[0...split_point].collect {|head| header_prep(head)}
|
96
|
+
output_headers = reader.headers[split_point+1..-1].collect {|head| head.strip}
|
97
|
+
|
98
|
+
reader.rewind
|
99
|
+
|
100
|
+
offset = input_headers.length+1
|
101
|
+
db = CouchRest.database!(training_datasource)
|
102
|
+
|
103
|
+
reader.each do |row|
|
104
|
+
inputs = {}
|
105
|
+
input_headers.each_with_index {|header,i| inputs[header] = row[i].strip}
|
106
|
+
outputs = {}
|
107
|
+
output_headers.each_with_index {|header,i| outputs[header] = row[i+offset].strip}
|
108
|
+
db.bulk_save_doc( {:inputs => inputs, :outputs => outputs})
|
109
|
+
end
|
110
|
+
|
111
|
+
db.bulk_save
|
112
|
+
|
113
|
+
end
|
114
|
+
|
115
|
+
|
116
|
+
def load_training_data!
|
117
|
+
db = CouchRest.database!(training_datasource)
|
118
|
+
result = db.view("#{@name}/test_cases")
|
119
|
+
@test_cases =
|
120
|
+
result["rows"].collect {|r| TestCase.new(
|
121
|
+
inputs: r["value"]["inputs"], outputs: r["value"]["outputs"])}
|
122
|
+
end
|
123
|
+
|
124
|
+
|
125
|
+
alias :generate :score
|
126
|
+
end
|
127
|
+
|
128
|
+
|
129
|
+
|
130
|
+
|
131
|
+
class TestCase
|
132
|
+
attr_accessor :inputs, :outputs
|
133
|
+
|
134
|
+
def initialize(options = {})
|
135
|
+
@inputs = options[:inputs] || {}
|
136
|
+
@outputs = options[:outputs] || {}
|
137
|
+
end
|
138
|
+
end
|
139
|
+
end
|
140
|
+
end
|
@@ -0,0 +1,54 @@
|
|
1
|
+
module AnswerFactory
|
2
|
+
module Machines
|
3
|
+
|
4
|
+
|
5
|
+
|
6
|
+
|
7
|
+
class SelectBySummedRank < Machine
|
8
|
+
|
9
|
+
def screen(batch, overriden_options={})
|
10
|
+
raise ArgumentError, "SelectBySummedRank#screen cannot process class #{batch.class}" unless
|
11
|
+
batch.kind_of?(Batch)
|
12
|
+
all_options = @options.merge(overriden_options)
|
13
|
+
|
14
|
+
criteria = all_options[:comparison_criteria] || shared_goals(batch)
|
15
|
+
return batch if criteria.empty?
|
16
|
+
|
17
|
+
scored = Hash.new(0)
|
18
|
+
incomparable = Set.new
|
19
|
+
|
20
|
+
criteria.each do |criterion|
|
21
|
+
scorable, unscorable = batch.partition {|a| a.scores.include?(criterion)}
|
22
|
+
incomparable += unscorable
|
23
|
+
ranked = scorable.sort_by {|a| a.scores[criterion]}
|
24
|
+
ranked.each_with_index do |a, index|
|
25
|
+
scored[a] += index
|
26
|
+
end
|
27
|
+
end
|
28
|
+
|
29
|
+
incomparable.each {|a| scored.delete(a)}
|
30
|
+
|
31
|
+
lowest_sum = scored.values.min
|
32
|
+
winners = batch.find_all {|a| scored[a] == lowest_sum }
|
33
|
+
|
34
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+
result = Batch.new
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incomparable.each {|a| result << a}
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+
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winners.each {|a| result << a unless result.include?(a)}
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return result
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+
end
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+
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+
|
42
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+
def all_goals(batch)
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+
(batch.collect {|a| a.scores.keys}).flatten.to_set.to_a
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+
end
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+
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46
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+
|
47
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+
def shared_goals(batch)
|
48
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+
batch.inject(all_goals(batch)) {|intersection, answer| intersection &= answer.scores.keys}
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49
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+
end
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+
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+
alias :generate :screen
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+
end
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53
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+
end
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+
end
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@@ -159,7 +159,7 @@ describe "Factory" do
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159
159
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:body => "Go away!", :status => [404, "Not Found"])
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Factory.couch_available?.should == false
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161
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|
162
|
-
f1 = Factory.new(name:"boo", couchdb_server:"http://127.0.0.1:
|
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+
f1 = Factory.new(name:"boo", couchdb_server:"http://127.0.0.1:5984/place")
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Factory.couch_available?.should == false
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end
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end
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@@ -174,6 +174,18 @@ describe "Factory" do
|
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it "should require authorization"
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end
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+
describe "training data" do
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+
before(:each) do
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+
FakeWeb.allow_net_connect = false
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+
end
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+
|
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|
+
it "should get the name of the :training_datasource from configatron" do
|
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+
Factory.new(name:"baz", couchdb_server:"http://127.0.0.1:5984").
|
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|
+
training_datasource.should == "http://127.0.0.1:5984/baz_training"
|
185
|
+
end
|
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|
+
|
187
|
+
end
|
188
|
+
|
177
189
|
describe "authorization" do
|
178
190
|
it "should be necessary to set up an admin account in couch"
|
179
191
|
|
@@ -24,6 +24,25 @@ describe "Workstation" do
|
|
24
24
|
end
|
25
25
|
end
|
26
26
|
|
27
|
+
describe "couchdb views documents" do
|
28
|
+
it "should respond to :couchdb_viewdoc" do
|
29
|
+
Workstation.new(:foo).should respond_to(:couchdb_viewdoc)
|
30
|
+
end
|
31
|
+
|
32
|
+
it "should return a Hash" do
|
33
|
+
Workstation.new(:foo).couchdb_viewdoc.should be_a_kind_of(Hash)
|
34
|
+
end
|
35
|
+
|
36
|
+
it "should have the right _id value" do
|
37
|
+
Workstation.new(:foo).couchdb_viewdoc["_id"].should == "_design/foo"
|
38
|
+
end
|
39
|
+
|
40
|
+
it "should include the correct map code for this Workstation" do
|
41
|
+
Workstation.new(:foo).couchdb_viewdoc[:views][:current][:map].should ==
|
42
|
+
"function(doc) { if(doc.location == 'foo') { emit(doc._id, doc); } }"
|
43
|
+
end
|
44
|
+
end
|
45
|
+
|
27
46
|
|
28
47
|
describe "capacity" do
|
29
48
|
it "should accept a #capacity attribute in initialization" do
|
@@ -15,7 +15,6 @@ end
|
|
15
15
|
|
16
16
|
describe "CouchDB stuff" do
|
17
17
|
before(:each) do
|
18
|
-
|
19
18
|
configatron.factory.couchdb.server = "http://127.0.0.1:5984"
|
20
19
|
configatron.factory.couchdb.name = "integration_test_db"
|
21
20
|
break("CouchDB is offline") unless Factory.couch_available?
|
@@ -24,6 +23,7 @@ describe "CouchDB stuff" do
|
|
24
23
|
|
25
24
|
after(:all) do
|
26
25
|
CouchRest.database!(@db_uri).delete!
|
26
|
+
CouchRest.database!("#{@db_uri}_training").delete!
|
27
27
|
end
|
28
28
|
|
29
29
|
|
@@ -37,7 +37,52 @@ describe "CouchDB stuff" do
|
|
37
37
|
Factory.couch_available?.should be false
|
38
38
|
FakeWeb.allow_net_connect = true
|
39
39
|
end
|
40
|
+
end
|
41
|
+
|
42
|
+
|
43
|
+
describe "Machine CouchDB interaction" do
|
44
|
+
before(:each) do
|
45
|
+
the_database_name = "#{@db_uri}_training"
|
46
|
+
@db = CouchRest.database!(the_database_name)
|
47
|
+
end
|
40
48
|
|
49
|
+
it "should accept :install_training_data_from_csv to populate a db from csv" do
|
50
|
+
configatron.temp do
|
51
|
+
configatron.factory.training_datasource = "http://127.0.0.1:5984/integration_test_db_training"
|
52
|
+
@db.save_doc(
|
53
|
+
{'_id' => "_design/tester",
|
54
|
+
views: { test_cases: { map:
|
55
|
+
"function(doc) { emit(doc._id, doc); }"}}})
|
56
|
+
|
57
|
+
@my_machine = Machines::EvaluateWithTestCases.new(name: :tester)
|
58
|
+
@my_machine.install_training_data_from_csv('./spec/fixtures/my_data_source.csv')
|
59
|
+
saved = @db.documents
|
60
|
+
saved["rows"].length.should == 4
|
61
|
+
end
|
62
|
+
end
|
63
|
+
|
64
|
+
it "should strip whitespace from all the training value strings" do
|
65
|
+
configatron.temp do
|
66
|
+
configatron.factory.training_datasource = "http://127.0.0.1:5984/integration_test_db_training"
|
67
|
+
@my_machine = Machines::EvaluateWithTestCases.new(name: :tester)
|
68
|
+
@my_machine.install_training_data_from_csv('./spec/fixtures/my_data_source.csv')
|
69
|
+
first_doc = @db.get(@db.documents["rows"][0]["id"])
|
70
|
+
first_doc["outputs"].each {|k,v| k.strip.should == k}
|
71
|
+
first_doc["outputs"].each {|k,v| v.strip.should == v}
|
72
|
+
|
73
|
+
first_doc["inputs"].each {|k,v| k.strip.should == k}
|
74
|
+
first_doc["inputs"].each {|k,v| v.strip.should == v}
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
it "should use load_training_data! to access the right view" do
|
79
|
+
configatron.temp do
|
80
|
+
configatron.factory.training_datasource = "http://127.0.0.1:5984/integration_test_db_training"
|
81
|
+
@my_machine = Machines::EvaluateWithTestCases.new(name: :tester)
|
82
|
+
@my_machine.load_training_data!
|
83
|
+
@my_machine.test_cases[0].inputs["x1:int"].should == "3"
|
84
|
+
end
|
85
|
+
end
|
41
86
|
end
|
42
87
|
|
43
88
|
describe "Batch reading and writing" do
|
@@ -87,6 +132,19 @@ describe "CouchDB stuff" do
|
|
87
132
|
|
88
133
|
describe "Workstations passing Batches around" do
|
89
134
|
|
135
|
+
describe "couchdb_create_view" do
|
136
|
+
before(:each) do
|
137
|
+
@ws_viewer = Workstation.new(:view_maker)
|
138
|
+
end
|
139
|
+
|
140
|
+
it "should save a view doc" do
|
141
|
+
response = @ws_viewer.couchdb_create_view
|
142
|
+
# "ok"=>true, "id"=>"_design/view_maker", "rev"=>"1-a813357133c1538c86168966b36f97bd"}
|
143
|
+
response["ok"].should == true
|
144
|
+
response["id"].should == "_design/view_maker"
|
145
|
+
end
|
146
|
+
end
|
147
|
+
|
90
148
|
describe "gathering" do
|
91
149
|
before(:each) do
|
92
150
|
@ws1 = ShipperStation.new(:this_place)
|