lazar-rest 1.0.0
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- checksums.yaml +7 -0
- data/.gitignore +13 -0
- data/.yardopts +5 -0
- data/ChangeLog +9 -0
- data/Gemfile +6 -0
- data/LICENSE +674 -0
- data/README.md +54 -0
- data/VERSION +1 -0
- data/api/api.json +1209 -0
- data/config.ru +5 -0
- data/lazar-rest.gemspec +26 -0
- data/lib/aa.rb +82 -0
- data/lib/api.rb +9 -0
- data/lib/compound.rb +64 -0
- data/lib/dataset.rb +47 -0
- data/lib/feature.rb +25 -0
- data/lib/lazar-rest.rb +37 -0
- data/lib/model.rb +50 -0
- data/lib/nanoparticle.rb +25 -0
- data/lib/report.rb +209 -0
- data/lib/substance.rb +25 -0
- data/lib/validation.rb +71 -0
- data/test/aa.rb +23 -0
- data/test/all.rb +5 -0
- data/test/api.rb +13 -0
- data/test/compound.rb +54 -0
- data/test/data/test_03_post_descriptor_file.result +152 -0
- data/test/descriptor.rb +48 -0
- data/test/model.rb +17 -0
- data/test/setup.rb +8 -0
- data/test/validation.rb +17 -0
- data/unicorn.rb +2 -0
- data/views/model_details.haml +121 -0
- metadata +176 -0
data/lib/substance.rb
ADDED
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@@ -0,0 +1,25 @@
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1
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# Get all substances
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2
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get "/substance/?" do
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3
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substances = Substance.all
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4
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case @accept
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5
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when "text/uri-list"
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6
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uri_list = substances.collect{|substance| uri("/substance/#{substance.id}")}
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7
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return uri_list.join("\n") + "\n"
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8
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when "application/json"
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9
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substances = JSON.parse substances.to_json
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10
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substances.each_index do |idx|
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11
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substances[idx][:URI] = uri("/substance/#{substances[idx]["_id"]["$oid"]}")
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end
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13
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return substances.to_json
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14
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else
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bad_request_error "Mime type #{@accept} is not supported."
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16
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end
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17
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end
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# Get a substance
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get "/substance/:id/?" do
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21
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substance = Substance.find :id => params[:id]
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22
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resource_not_found_error "Substance with id: #{params[:id]} not found." unless substance
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23
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substance[:URI] = uri("/substance/#{substance.id}")
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24
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return substance.to_json
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25
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+
end
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data/lib/validation.rb
ADDED
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@@ -0,0 +1,71 @@
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1
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# All available validation types
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VALIDATION_TYPES = ["repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation"]
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3
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4
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# Get a list of ayll possible validation types
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5
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# @param [Header] Accept one of text/uri-list, application/json
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6
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# @return [text/uri-list] URI list of all validation types
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7
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get "/validation/?" do
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8
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uri_list = VALIDATION_TYPES.collect{|validationtype| uri("/validation/#{validationtype}")}
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9
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case @accept
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10
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when "text/uri-list"
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11
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return uri_list.join("\n") + "\n"
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12
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when "application/json"
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13
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+
return uri_list.to_json
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14
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+
else
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15
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+
bad_request_error "Mime type #{@accept} is not supported."
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16
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+
end
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17
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end
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18
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+
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# Get a list of all validations
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20
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# @param [Header] Accept one of text/uri-list, application/json
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21
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# @param [Path] Validationtype One of "repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation"
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22
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# @return [text/uri-list] list of all validations of a validation type
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23
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get "/validation/:validationtype/?" do
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24
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bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype]
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25
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case params[:validationtype]
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26
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when "repeatedcrossvalidation"
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27
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validations = Validation::RepeatedCrossValidation.all
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28
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when "leaveoneout"
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29
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validations = Validation::LeaveOneOut.all
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30
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when "crossvalidation"
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31
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+
validations = Validation::CrossValidation.all
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32
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when "regressioncrossvalidation"
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33
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validations = Validation::RegressionCrossValidation.all
|
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34
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+
end
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35
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+
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36
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+
case @accept
|
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37
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when "text/uri-list"
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38
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uri_list = validations.collect{|validation| uri("/validation/#{params[:validationtype]}/#{validation.id}")}
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39
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+
return uri_list.join("\n") + "\n"
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40
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+
when "application/json"
|
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41
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+
validations = JSON.parse validations.to_json
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42
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+
validations.each_index do |idx|
|
|
43
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+
validations[idx][:URI] = uri("/validation/#{params[:validationtype]}/#{validations[idx]["_id"]["$oid"]}")
|
|
44
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+
end
|
|
45
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+
return validations.to_json
|
|
46
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+
else
|
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47
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+
bad_request_error "Mime type #{@accept} is not supported."
|
|
48
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+
end
|
|
49
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+
end
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50
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+
|
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51
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+
# Get validation representation
|
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52
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+
get "/validation/:validationtype/:id/?" do
|
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53
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+
bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype]
|
|
54
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+
case params[:validationtype]
|
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55
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+
when "repeatedcrossvalidation"
|
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56
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+
validation = Validation::RepeatedCrossValidation.find params[:id]
|
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57
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+
when "leaveoneout"
|
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58
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+
validation = Validation::LeaveOneOut.find params[:id]
|
|
59
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+
when "crossvalidation"
|
|
60
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+
validation = Validation::CrossValidation.find params[:id]
|
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61
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+
when "regressioncrossvalidation"
|
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62
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+
validation = Validation::RegressionCrossValidation.find params[:id]
|
|
63
|
+
end
|
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64
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+
|
|
65
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+
resource_not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation
|
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66
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+
#model[:URI] = uri("/model/#{model.id}")
|
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67
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+
#model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id]
|
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68
|
+
#model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id
|
|
69
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+
#model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id
|
|
70
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+
return validation.to_json
|
|
71
|
+
end
|
data/test/aa.rb
ADDED
|
@@ -0,0 +1,23 @@
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1
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+
require_relative "setup.rb"
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2
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+
|
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3
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+
class AATest < MiniTest::Test
|
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4
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+
|
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5
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+
def test_0_login
|
|
6
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+
res = RestClientWrapper.post(File.join($host,"aa/authenticate"),{:username=>"guest", :password => "guest"},{:Accept => "text/plain"})
|
|
7
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+
assert_equal res.code, 200
|
|
8
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+
assert_equal res.size, 62
|
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9
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+
@@token = res
|
|
10
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+
end
|
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11
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+
|
|
12
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+
def test_1_logout
|
|
13
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+
assert @@token
|
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14
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+
assert_equal @@token.size, 62
|
|
15
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+
res = RestClientWrapper.post(File.join($host,"aa/logout"),{:subjectid=>@@token},{:Accept => "text/plain"})
|
|
16
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+
assert_equal res.code, 200
|
|
17
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+
assert_equal res, "Successfully logged out. \n"
|
|
18
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+
res = RestClientWrapper.post(File.join($host,"aa/logout"),{:subjectid=>@@token},{:Accept => "text/plain"})
|
|
19
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+
assert_equal res.code, 200
|
|
20
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+
assert_equal res, "Logout failed.\n"
|
|
21
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+
end
|
|
22
|
+
|
|
23
|
+
end
|
data/test/all.rb
ADDED
data/test/api.rb
ADDED
data/test/compound.rb
ADDED
|
@@ -0,0 +1,54 @@
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|
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1
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+
require_relative "setup.rb"
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2
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+
|
|
3
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+
$compound_uri = "#{$host}/compound"
|
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4
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+
$compound = ["InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"]
|
|
5
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+
|
|
6
|
+
class CompoundTest < MiniTest::Test
|
|
7
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+
|
|
8
|
+
def test_00_get_inchi
|
|
9
|
+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => 'chemical/x-inchi'}
|
|
10
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+
assert_equal res.code, 200
|
|
11
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+
assert_equal res, "InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H"
|
|
12
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+
end
|
|
13
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+
|
|
14
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+
def test_01_get_smiles
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|
15
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+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "chemical/x-daylight-smiles"}
|
|
16
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+
assert_equal res.code, 200
|
|
17
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+
assert_equal res, "c1ccccc1"
|
|
18
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+
end
|
|
19
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+
|
|
20
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+
def test_02_get_sdf
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|
21
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+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "chemical/x-mdl-sdfile"}
|
|
22
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+
assert_equal res.code, 200
|
|
23
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+
assert res.include?(" 6 12 1 0 0 0 0\nM END\n$$$")
|
|
24
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+
end
|
|
25
|
+
|
|
26
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+
def test_03_get_png
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|
27
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+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "image/png"}
|
|
28
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+
assert_equal res.code, 200
|
|
29
|
+
assert_equal "image/png", res.headers[:content_type]
|
|
30
|
+
end
|
|
31
|
+
|
|
32
|
+
def test_04_get_svg
|
|
33
|
+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "image/svg+xml"}
|
|
34
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+
assert_equal res.code, 200
|
|
35
|
+
assert res.include?("<svg version=")
|
|
36
|
+
end
|
|
37
|
+
|
|
38
|
+
def test_05_get_json
|
|
39
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+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "application/json"}
|
|
40
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+
assert_equal res.code, 200
|
|
41
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+
js = JSON.parse res
|
|
42
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+
assert_equal js["chemblid"], "CHEMBL277500"
|
|
43
|
+
assert_equal js["names"].first, "BENZENE"
|
|
44
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+
assert_equal js["names"][6], "71-43-2"
|
|
45
|
+
end
|
|
46
|
+
|
|
47
|
+
def test_06_get_names
|
|
48
|
+
res = RestClientWrapper.get File.join($compound_uri, $compound[0]), {}, {:accept => "text/plain"}
|
|
49
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+
assert_equal res.code, 200
|
|
50
|
+
assert res.include?("Benzene")
|
|
51
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+
assert res.include?("401765_ALDRICH")
|
|
52
|
+
end
|
|
53
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+
|
|
54
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+
end
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|
@@ -0,0 +1,152 @@
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1
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+
[
|
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2
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+
{
|
|
3
|
+
"SMILES": "CC=O",
|
|
4
|
+
"Openbabel.logP": "0.2052",
|
|
5
|
+
"Cdk.AtomCount.nAtom": "7",
|
|
6
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
7
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
8
|
+
"Cdk.CarbonTypes.C1SP2": "1",
|
|
9
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
10
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
11
|
+
"Cdk.CarbonTypes.C1SP3": "1",
|
|
12
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
13
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
14
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
15
|
+
"Joelib.LogP": "0.7679"
|
|
16
|
+
},
|
|
17
|
+
{
|
|
18
|
+
"SMILES": "CC(=O)Nc1ccc2c(c1)Cc1c2cccc1",
|
|
19
|
+
"Openbabel.logP": "3.2892",
|
|
20
|
+
"Cdk.AtomCount.nAtom": "30",
|
|
21
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
22
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
23
|
+
"Cdk.CarbonTypes.C1SP2": "1",
|
|
24
|
+
"Cdk.CarbonTypes.C2SP2": "8",
|
|
25
|
+
"Cdk.CarbonTypes.C3SP2": "4",
|
|
26
|
+
"Cdk.CarbonTypes.C1SP3": "1",
|
|
27
|
+
"Cdk.CarbonTypes.C2SP3": "1",
|
|
28
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
29
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
30
|
+
"Joelib.LogP": "5.3165"
|
|
31
|
+
},
|
|
32
|
+
{
|
|
33
|
+
"SMILES": "NC(=O)/C(=C\\c1ccc(o1)[N+](=O)[O-])/c1ccco1",
|
|
34
|
+
"Openbabel.logP": "3.0302",
|
|
35
|
+
"Cdk.AtomCount.nAtom": "26",
|
|
36
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
37
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
38
|
+
"Cdk.CarbonTypes.C1SP2": "3",
|
|
39
|
+
"Cdk.CarbonTypes.C2SP2": "7",
|
|
40
|
+
"Cdk.CarbonTypes.C3SP2": "1",
|
|
41
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
42
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
43
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
44
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
45
|
+
"Joelib.LogP": "3.6734"
|
|
46
|
+
},
|
|
47
|
+
{
|
|
48
|
+
"SMILES": "Nc1n[nH]cn1",
|
|
49
|
+
"Openbabel.logP": "-0.0319",
|
|
50
|
+
"Cdk.AtomCount.nAtom": "10",
|
|
51
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
52
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
53
|
+
"Cdk.CarbonTypes.C1SP2": "0",
|
|
54
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
55
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
56
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
57
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
58
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
59
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
60
|
+
"Joelib.LogP": "0.7337"
|
|
61
|
+
},
|
|
62
|
+
{
|
|
63
|
+
"SMILES": "[O-][Br](=O)=O.[K+]",
|
|
64
|
+
"Openbabel.logP": "0.4892",
|
|
65
|
+
"Cdk.AtomCount.nAtom": "2",
|
|
66
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
67
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
68
|
+
"Cdk.CarbonTypes.C1SP2": "0",
|
|
69
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
70
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
71
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
72
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
73
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
74
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
75
|
+
"Joelib.LogP": "-5.9945"
|
|
76
|
+
},
|
|
77
|
+
{
|
|
78
|
+
"SMILES": "[Cl-].[Cl-].[Cd+2]",
|
|
79
|
+
"Openbabel.logP": "-5.9945",
|
|
80
|
+
"Cdk.AtomCount.nAtom": "3",
|
|
81
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
82
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
83
|
+
"Cdk.CarbonTypes.C1SP2": "0",
|
|
84
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
85
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
86
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
87
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
88
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
89
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
90
|
+
"Joelib.LogP": "-0.2597"
|
|
91
|
+
},
|
|
92
|
+
{
|
|
93
|
+
"SMILES": "[O-]S(=O)(=O)[O-].[Cd+2]",
|
|
94
|
+
"Openbabel.logP": "-0.2597",
|
|
95
|
+
"Cdk.AtomCount.nAtom": "6",
|
|
96
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
97
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
98
|
+
"Cdk.CarbonTypes.C1SP2": "0",
|
|
99
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
100
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
101
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
102
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
103
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
104
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
105
|
+
"Joelib.LogP": "5.0725"
|
|
106
|
+
},
|
|
107
|
+
{
|
|
108
|
+
"SMILES": "OC(=O)CSc1nc(cc(n1)Cl)Nc1cccc(c1C)C",
|
|
109
|
+
"Openbabel.logP": "3.7401",
|
|
110
|
+
"Cdk.AtomCount.nAtom": "35",
|
|
111
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
112
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
113
|
+
"Cdk.CarbonTypes.C1SP2": "3",
|
|
114
|
+
"Cdk.CarbonTypes.C2SP2": "5",
|
|
115
|
+
"Cdk.CarbonTypes.C3SP2": "2",
|
|
116
|
+
"Cdk.CarbonTypes.C1SP3": "3",
|
|
117
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
118
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
119
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
120
|
+
"Joelib.LogP": "2.2807"
|
|
121
|
+
},
|
|
122
|
+
{
|
|
123
|
+
"SMILES": "COCCl",
|
|
124
|
+
"Openbabel.logP": "0.8291",
|
|
125
|
+
"Cdk.AtomCount.nAtom": "9",
|
|
126
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
127
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
128
|
+
"Cdk.CarbonTypes.C1SP2": "0",
|
|
129
|
+
"Cdk.CarbonTypes.C2SP2": "0",
|
|
130
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
131
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
132
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
133
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
134
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
135
|
+
"Joelib.LogP": "2.5399"
|
|
136
|
+
},
|
|
137
|
+
{
|
|
138
|
+
"SMILES": "C=CC(=C)Cl",
|
|
139
|
+
"Openbabel.logP": "1.9249",
|
|
140
|
+
"Cdk.AtomCount.nAtom": "10",
|
|
141
|
+
"Cdk.CarbonTypes.C1SP1": "0",
|
|
142
|
+
"Cdk.CarbonTypes.C2SP1": "0",
|
|
143
|
+
"Cdk.CarbonTypes.C1SP2": "2",
|
|
144
|
+
"Cdk.CarbonTypes.C2SP2": "2",
|
|
145
|
+
"Cdk.CarbonTypes.C3SP2": "0",
|
|
146
|
+
"Cdk.CarbonTypes.C1SP3": "0",
|
|
147
|
+
"Cdk.CarbonTypes.C2SP3": "0",
|
|
148
|
+
"Cdk.CarbonTypes.C3SP3": "0",
|
|
149
|
+
"Cdk.CarbonTypes.C4SP3": "0",
|
|
150
|
+
"Joelib.LogP": null
|
|
151
|
+
}
|
|
152
|
+
]
|
data/test/descriptor.rb
ADDED
|
@@ -0,0 +1,48 @@
|
|
|
1
|
+
require_relative "setup.rb"
|
|
2
|
+
|
|
3
|
+
$host = "#{$host}"
|
|
4
|
+
|
|
5
|
+
|
|
6
|
+
class DescriptorTest < MiniTest::Test
|
|
7
|
+
|
|
8
|
+
def test_00_get_descriptors
|
|
9
|
+
result = RestClientWrapper.get File.join($host, "compound/descriptor"), {}, {:accept => "text/plain"}
|
|
10
|
+
assert_equal result.code, 200
|
|
11
|
+
assert result.include?("Joelib.KierShape1: JOELIb does not provide meaningful descriptions, see java/JoelibDescriptors.java for details.\nJoelib.KierShape2: JOELIb does not provide meaningful descriptions, see java/JoelibDescriptors.java for details."), "Descriptor list is not complete."
|
|
12
|
+
assert_equal 355, result.lines.count
|
|
13
|
+
end
|
|
14
|
+
|
|
15
|
+
def test_01_get_descriptor
|
|
16
|
+
result = RestClientWrapper.get File.join($host, "compound/descriptor", "Openbabel.MW"), {}, {:accept => "text/plain"}
|
|
17
|
+
assert_equal result.code, 200
|
|
18
|
+
assert_equal result, "Molecular Weight filter"
|
|
19
|
+
end
|
|
20
|
+
|
|
21
|
+
def test_03_get_descriptor_id
|
|
22
|
+
result = RestClientWrapper.get File.join($host, "compound/descriptor", "Openbabel.HBA1"), {}, {:accept => "application/json"}
|
|
23
|
+
assert_equal result.code, 200
|
|
24
|
+
json = JSON.parse(result)
|
|
25
|
+
assert_equal json["description"], "Number of Hydrogen Bond Acceptors 1 (JoelLib)"
|
|
26
|
+
bsonid = json["_id"]["$oid"]
|
|
27
|
+
result = RestClientWrapper.get File.join($host, "compound/descriptor", bsonid), {}, {:accept => "application/json"}
|
|
28
|
+
json = JSON.parse(result)
|
|
29
|
+
assert_equal json["name"], "Openbabel.HBA1"
|
|
30
|
+
assert_equal json["numeric"], true
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
def test_04_post_descriptor
|
|
34
|
+
result = RestClientWrapper.post File.join($host, "compound/descriptor"), {:identifier => "CC(=O)CC(C)C#N", :descriptor => "Joelib.LogP"}, {:accept => "application/csv"}
|
|
35
|
+
assert_equal result.code, 200
|
|
36
|
+
assert_equal "SMILES,CC(=O)CC(C)C#N\n\"Joelib.LogP\",2.65908", result
|
|
37
|
+
end
|
|
38
|
+
|
|
39
|
+
# currently not applicable
|
|
40
|
+
#def test_05_post_descriptor_file
|
|
41
|
+
# file = File.join(DATA_DIR, "hamster_carcinogenicity.mini.csv")
|
|
42
|
+
# result = RestClientWrapper.post File.join($host, "compound/descriptor"), {:file => File.open(file), :descriptor => "Openbabel.logP,Cdk.AtomCount,Cdk.CarbonTypes,Joelib.LogP"}, {:accept => "application/json"}
|
|
43
|
+
# assert_equal result.code, 200
|
|
44
|
+
# proof_result = File.read(File.join(REST_DATA_DIR, "test_03_post_descriptor_file.result"))
|
|
45
|
+
# assert_equal result, proof_result.strip
|
|
46
|
+
#end
|
|
47
|
+
|
|
48
|
+
end
|
data/test/model.rb
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
require_relative "setup.rb"
|
|
2
|
+
|
|
3
|
+
$model_uri = "#{$host}/model"
|
|
4
|
+
class ModelTest < MiniTest::Test
|
|
5
|
+
|
|
6
|
+
def test_00_get_urilist
|
|
7
|
+
res = RestClientWrapper.get $model_uri, {}, {:accept => "text/uri-list"}
|
|
8
|
+
assert_equal res.code, 200
|
|
9
|
+
end
|
|
10
|
+
|
|
11
|
+
def test_01_get_400
|
|
12
|
+
assert_raises OpenTox::BadRequestError do
|
|
13
|
+
res = OpenTox::RestClientWrapper.get $model_uri, {}, {:accept => "text/notimplemented-type"}
|
|
14
|
+
end
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
end
|
data/test/setup.rb
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
require 'minitest/autorun'
|
|
2
|
+
|
|
3
|
+
require_relative '../../lazar/lib/lazar.rb'
|
|
4
|
+
require_relative '../../lazar/test/setup.rb'
|
|
5
|
+
$host = "https://enm.in-silico.ch"
|
|
6
|
+
include OpenTox
|
|
7
|
+
REST_TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
|
|
8
|
+
REST_DATA_DIR ||= File.join(REST_TEST_DIR,"data")
|
data/test/validation.rb
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
require_relative "setup.rb"
|
|
2
|
+
|
|
3
|
+
$validation_uri = "#{$host}/validation"
|
|
4
|
+
class ModelTest < MiniTest::Test
|
|
5
|
+
|
|
6
|
+
def test_00_get_urilist
|
|
7
|
+
res = RestClientWrapper.get $validation_uri, {}, {:accept => "text/uri-list"}
|
|
8
|
+
assert_equal res.code, 200
|
|
9
|
+
end
|
|
10
|
+
|
|
11
|
+
def test_01_get_400
|
|
12
|
+
assert_raises OpenTox::BadRequestError do
|
|
13
|
+
res = OpenTox::RestClientWrapper.get $validation_uri, {}, {:accept => "text/notimplemented-type"}
|
|
14
|
+
end
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
end
|