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#DATA = ["LOAEL-mol", "LOAEL-mg", "MOU"]
DATA = ["LOAEL-mol"]
#DATA = ["MOU"]
URIS = {
"LOAEL-mol"=>{
:dataset_uri=>"http://localhost:8083/dataset/3da90c55-0388-42a0-8ada-978abe4a515c",
:prediction_feature=>"http://localhost:8084/feature/2a74d78d-5b3d-438c-a1e5-6cfb16bd9354",
:new_feature_dataset_uri=>"http://localhost:8083/dataset/7de04de4-41ce-4528-97c2-fd92fbb4d0b8",
:orig_feature_dataset_uri=>"http://localhost:8083/dataset/e9016641-dddb-434f-bb05-63d80a37679a",
:all_feature_dataset_uri=>"http://localhost:8083/dataset/bc551e60-b2e7-4fb9-9aa3-52433ac1358c",
:ob_feature_dataset_uri=>"http://localhost:8083/dataset/ac44674f-efa9-4cf9-b1ff-37e63e3cf8aa",
},
"LOAEL-mg"=>{
:dataset_uri=>"http://localhost:8083/dataset/4f3b9de4-0494-4339-8ebd-e6c6c1984a23",
:prediction_feature=>"http://localhost:8084/feature/ba5b0f78-36bc-4ac3-8020-9d8b2ca3bd13",
:new_feature_dataset_uri=>"http://localhost:8083/dataset/7de04de4-41ce-4528-97c2-fd92fbb4d0b8",
:orig_feature_dataset_uri=>"http://localhost:8083/dataset/e9016641-dddb-434f-bb05-63d80a37679a",
},
"MOU"=>{
# :dataset_uri=>"http://localhost:8083/dataset/f0af478a-51e6-41a5-adb2-d1a9bedf8981",
# :prediction_feature=>"http://localhost:8084/feature/432f18c5-ff8f-4ff2-a1cc-cbda1c43cff9",
# :test_dataset_uri=>"http://localhost:8083/dataset/a5c39a5d-8747-495a-8d30-6ee9abdd5f3b",
# :new_feature_dataset_uri=>"http://localhost:8083/dataset/8d324c7d-e6fe-4807-b2f8-e851750b959d",
# :orig_feature_dataset_uri=>"http://localhost:8083/dataset/cc651943-886c-4290-b346-41d1c951476a",
},
}
def info(d)
puts d.uri
if d.is_a?(OpenTox::Dataset)
puts "#{d.compounds.size} compounds"
puts "#{d.features.size} features"
# puts d.features.collect{|f| "#{f.title} : #{f[RDF::type]}"}.inspect
end
end
def plz_add(msg)
$stderr.puts "please add to config.rb: #{msg}"
abort
end
def dataset_uri(d)
if URIS[d] and URIS[d][:dataset_uri]
URIS[d][:dataset_uri]
else
dataset = OpenTox::Dataset.new
dataset.upload File.join("data/02/#{d}_endpoint.csv")
info(dataset)
plz_add "dataset_uri #{dataset.uri} and prediction_feature #{dataset.features.first.uri}"
end
end
def prediction_feature(d)
if URIS[d] and URIS[d][:prediction_feature]
URIS[d][:prediction_feature]
else
plz_add "prediction_feature by uploading dataset"
end
end
def test_dataset_uri(d)
if URIS[d] and URIS[d][:test_dataset_uri]
URIS[d][:test_dataset_uri]
else
pred_feat = prediction_feature(d)
dataset = OpenTox::Dataset.new
dataset.upload File.join("data/#{d}_test.csv")
info(dataset)
raise "uri of test dataset feature != prediction_feature" unless dataset.features.first.uri==pred_feat
plz_add "test_datsaet_uri #{dataset.uri}"
end
end
def all_feature_dataset_uri(d)
if URIS[d] and URIS[d][:all_feature_dataset_uri]
URIS[d][:all_feature_dataset_uri]
else
u_dataset = OpenTox::Dataset.new
u_dataset.upload File.join("data/03/#{d}_uniq.csv")
puts "Unique Dataset: "+u_dataset.uri
info(u_dataset)
@descriptors = OpenTox::Algorithm::Descriptor.physchem_descriptors.keys - ["Cdk.IPMolecularLearning"]
all_feat_uri = wait_for_task(OpenTox::RestClientWrapper.post("http://localhost:8081/algorithm/descriptor/physchem",{:dataset_uri => u_dataset.uri, :descriptors => @descriptors}))
f_dataset = OpenTox::Dataset.new all_feat_uri
info(f_dataset)
plz_add "all_feature_dataset_uri #{all_feat_uri}"
end
end
def ob_feature_dataset_uri(d)
if URIS[d] and URIS[d][:ob_feature_dataset_uri]
URIS[d][:ob_feature_dataset_uri]
else
u_dataset = OpenTox::Dataset.new
u_dataset.upload File.join("data/03/#{d}_uniq.csv")
puts "Unique Dataset: "+u_dataset.uri
info(u_dataset)
@descriptors = OpenTox::Algorithm::Descriptor.physchem_descriptors.keys.keep_if{|x| x=~/^Openbabel\./}
ob_feat_uri = wait_for_task(OpenTox::RestClientWrapper.post("http://localhost:8081/algorithm/descriptor/physchem",{:dataset_uri => u_dataset.uri, :descriptors => @descriptors}))
f_dataset = OpenTox::Dataset.new ob_feat_uri
info(f_dataset)
plz_add "ob_feature_dataset_uri #{ob_feat_uri}"
end
end
def new_feature_dataset_uri(d)
if URIS[d] and URIS[d][:new_feature_dataset_uri]
URIS[d][:new_feature_dataset_uri]
else
u_dataset = OpenTox::Dataset.new
u_dataset.upload File.join("data/03/#{d}_uniq.csv")
puts "Unique Dataset: "+u_dataset.uri
info(u_dataset)
feature_names = File.open("data/04/#{d}.feature_names","r").read.chomp.split(",")
puts "Features: "+feature_names.inspect
new_feat_uri = wait_for_task(OpenTox::RestClientWrapper.post("http://localhost:8081/algorithm/descriptor/physchem",{:dataset_uri => u_dataset.uri, :descriptors => feature_names}))
f_dataset = OpenTox::Dataset.new new_feat_uri
info(f_dataset)
plz_add "feature_dataset_uri #{new_feat_uri}"
end
end
def orig_feature_dataset_uri(d)
if URIS[d] and URIS[d][:orig_feature_dataset_uri]
URIS[d][:orig_feature_dataset_uri]
else
f = OpenTox::Dataset.new
f.upload File.join("data/02/#{d}_orig-features.csv")
info(f)
plz_add "orig_feature_dataset_uri #{f.uri}"
end
end
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