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/unicorn.rb
ADDED
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%html
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%head
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%body
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%b Model:
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%br
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Source:
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%a{:href => model.source}
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= model.source
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%br
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- model.classification? ? type = "Classification" : type = "Regression"
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= "Type:\t"
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= type
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%br
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- training_dataset = OpenTox::Dataset.find model.training_dataset.id
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= "Training compounds:\t"
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= training_dataset.compounds.size
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%br
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%p
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- if type == "Classification"
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%b Independent crossvalidations:
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- else
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%b Independent crossvalidations (-log10 transformed):
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- model.crossvalidations.each do |crossvalidation|
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%br
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= "Num folds:\t"
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= crossvalidation.folds
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%br
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= "Num instances:\t"
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= crossvalidation.nr_instances
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%br
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= "Num unpredicted"
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= crossvalidation.nr_unpredicted
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- if model.classification?
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%br
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= "Accuracy:\t"
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= crossvalidation.accuracy.round(3) if crossvalidation.accuracy
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%br
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- if crossvalidation.true_rate
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= "True positive rate:\t"
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= crossvalidation.true_rate["active"].round(3) if crossvalidation.true_rate["active"]
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%br
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= "True negative rate:\t"
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= crossvalidation.true_rate["inactive"].round(3) if crossvalidation.true_rate["inactive"]
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%br
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- if crossvalidation.predictivity
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= "Positive predictive value:\t"
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= crossvalidation.predictivity["active"].round(3) if crossvalidation.predictivity["active"]
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%br
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= "Negative predictive value:\t"
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= crossvalidation.predictivity["inactive"].round(3) if crossvalidation.predictivity["inactive"]
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%br
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%br
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%b Confusion Matrix:
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%table{:class => "table table-condensed table-borderless", :style=>"width:20%;"}
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%tbody
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%tr
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%td
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%td
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%td
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%b actual
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%td
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%td
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%tr
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%td
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%td
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%td active
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%td inactive
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-#%td total
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%tr
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%td
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%b predicted
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%td active
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%td
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=crossvalidation.confusion_matrix[0][0]
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%td
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=crossvalidation.confusion_matrix[0][1]
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-#%td
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=crossvalidation.confusion_matrix[0][0]+crossvalidation.confusion_matrix[0][1]
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%tr
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%td
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%td inactive
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%td
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=crossvalidation.confusion_matrix[1][0]
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%td
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=crossvalidation.confusion_matrix[1][1]
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-#%td
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=crossvalidation.confusion_matrix[1][0]+crossvalidation.confusion_matrix[1][1]
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-#%tr
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%td
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%td total
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%td
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=crossvalidation.confusion_matrix[0][0]+crossvalidation.confusion_matrix[1][0]
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%td
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=crossvalidation.confusion_matrix[0][1]+crossvalidation.confusion_matrix[1][1]
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%td
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-#= "Confusion Matrix:\t"
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-#= crossvalidation.confusion_matrix
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/= "Confidence plot:"
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/%p.plot
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/ %img{:src=>"confp#{crossvalidation.id}.svg"}
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- if model.regression?
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%br
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105
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= "Root mean squared error:\t"
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= crossvalidation.rmse.round(3) if crossvalidation.rmse
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%br
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= "Mean absolute error:\t"
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= crossvalidation.mae.round(3) if crossvalidation.mae
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%br
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= "R square:\t"
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= crossvalidation.r_squared.round(3) if crossvalidation.r_squared
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%br
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/= "Confidence plot:"
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/%p.plot
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/ %img{:src=>"/confp#{crossvalidation.id}.svg"}
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/%br
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/= "Correlation plot"
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/%p.plot
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/ %img{:src=>"/corrp#{crossvalidation.id}.svg"}
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metadata
ADDED
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@@ -0,0 +1,176 @@
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1
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--- !ruby/object:Gem::Specification
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2
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name: lazar-rest
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version: !ruby/object:Gem::Version
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version: 1.0.0
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platform: ruby
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authors:
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- Christoph Helma
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8
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- Micha Rautenberg
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9
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- Denis Gebele
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10
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autorequire:
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11
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bindir: bin
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12
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cert_chain: []
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13
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date: 2016-11-03 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: lazar
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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26
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- - ">="
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27
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- !ruby/object:Gem::Version
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28
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version: '0'
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- !ruby/object:Gem::Dependency
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30
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name: qsar-report
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requirement: !ruby/object:Gem::Requirement
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32
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requirements:
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33
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- - ">="
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34
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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37
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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40
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- - ">="
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41
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- !ruby/object:Gem::Version
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42
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version: '0'
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43
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- !ruby/object:Gem::Dependency
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44
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name: sinatra
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45
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requirement: !ruby/object:Gem::Requirement
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46
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requirements:
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47
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- - ">="
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48
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- !ruby/object:Gem::Version
|
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49
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version: '0'
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50
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type: :runtime
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51
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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54
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- - ">="
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55
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- !ruby/object:Gem::Version
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56
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version: '0'
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57
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- !ruby/object:Gem::Dependency
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58
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name: haml
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59
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requirement: !ruby/object:Gem::Requirement
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60
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requirements:
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61
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- - ">="
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62
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- !ruby/object:Gem::Version
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63
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version: '0'
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64
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type: :runtime
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65
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: sass
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73
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requirement: !ruby/object:Gem::Requirement
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requirements:
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75
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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84
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version: '0'
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85
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- !ruby/object:Gem::Dependency
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86
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name: unicorn
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87
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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89
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- - ">="
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90
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- !ruby/object:Gem::Version
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91
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version: '0'
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92
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type: :runtime
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93
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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95
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requirements:
|
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96
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- - ">="
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97
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+
- !ruby/object:Gem::Version
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98
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version: '0'
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99
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- !ruby/object:Gem::Dependency
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100
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name: rack-cors
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101
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requirement: !ruby/object:Gem::Requirement
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102
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requirements:
|
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103
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- - ">="
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104
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- !ruby/object:Gem::Version
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105
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version: '0'
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106
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type: :runtime
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107
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prerelease: false
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108
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version_requirements: !ruby/object:Gem::Requirement
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109
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requirements:
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110
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- - ">="
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111
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- !ruby/object:Gem::Version
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112
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version: '0'
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113
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description: REST Interface for Lazar Toxicology Predictions
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114
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email:
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115
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- supprot@in-silico.ch
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116
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executables: []
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117
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extensions: []
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118
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extra_rdoc_files: []
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119
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files:
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120
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- ".gitignore"
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121
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- ".yardopts"
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122
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- ChangeLog
|
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123
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- Gemfile
|
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124
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- LICENSE
|
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125
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- README.md
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126
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- VERSION
|
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127
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+
- api/api.json
|
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128
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+
- config.ru
|
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129
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+
- lazar-rest.gemspec
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130
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+
- lib/aa.rb
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131
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- lib/api.rb
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132
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- lib/compound.rb
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133
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- lib/dataset.rb
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134
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- lib/feature.rb
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135
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- lib/lazar-rest.rb
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136
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- lib/model.rb
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137
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- lib/nanoparticle.rb
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138
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- lib/report.rb
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139
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- lib/substance.rb
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140
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- lib/validation.rb
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141
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- test/aa.rb
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142
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- test/all.rb
|
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143
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- test/api.rb
|
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144
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- test/compound.rb
|
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145
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- test/data/test_03_post_descriptor_file.result
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146
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- test/descriptor.rb
|
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147
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+
- test/model.rb
|
|
148
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+
- test/setup.rb
|
|
149
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+
- test/validation.rb
|
|
150
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+
- unicorn.rb
|
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151
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+
- views/model_details.haml
|
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152
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+
homepage: http://github.com/opentox/lazar-rest
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153
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licenses:
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154
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- GPL-3
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155
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metadata: {}
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156
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post_install_message:
|
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157
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rdoc_options: []
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158
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require_paths:
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|
159
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+
- lib
|
|
160
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required_ruby_version: !ruby/object:Gem::Requirement
|
|
161
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+
requirements:
|
|
162
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+
- - ">="
|
|
163
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+
- !ruby/object:Gem::Version
|
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164
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+
version: 2.0.0
|
|
165
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+
required_rubygems_version: !ruby/object:Gem::Requirement
|
|
166
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requirements:
|
|
167
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+
- - ">="
|
|
168
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+
- !ruby/object:Gem::Version
|
|
169
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version: '0'
|
|
170
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requirements: []
|
|
171
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+
rubyforge_project: lazar-rest
|
|
172
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+
rubygems_version: 2.5.1
|
|
173
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+
signing_key:
|
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174
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+
specification_version: 4
|
|
175
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+
summary: lazar-rest
|
|
176
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+
test_files: []
|