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|
ENV['FMINER_SMARTS'] = 'true'
ENV['FMINER_NO_AROMATIC'] = 'true'
ENV['FMINER_PVALUES'] = 'true'
@@fminer = Bbrc::Bbrc.new
get '/fminer/?' do
owl = OpenTox::Owl.create 'Algorithm', url_for('/fminer',:full)
owl.set 'title',"fminer"
owl.set 'creator',"http://github.com/amaunz/fminer2"
owl.parameters = {
"Dataset URI" => { :scope => "mandatory", :value => "dataset_uri" },
"Feature URI for dependent variable" => { :scope => "mandatory", :value => "feature_uri" }
}
rdf = owl.rdf
File.open('public/fminer.owl', 'w') {|f| f.print rdf}
response['Content-Type'] = 'application/rdf+xml'
rdf
end
post '/fminer/?' do
halt 404, "Please submit a dataset_uri." unless params[:dataset_uri] and !params[:dataset_uri].nil?
halt 404, "Please submit a feature_uri." unless params[:feature_uri] and !params[:feature_uri].nil?
LOGGER.debug "Dataset: " + params[:dataset_uri]
LOGGER.debug "Endpoint: " + params[:feature_uri]
feature_uri = params[:feature_uri]
begin
LOGGER.debug "Retrieving #{params[:dataset_uri]}"
training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}"
rescue
LOGGER.error "Dataset #{params[:dataset_uri]} not found"
halt 404, "Dataset #{params[:dataset_uri]} not found." if training_dataset.nil?
end
halt 404, "No feature #{params[:feature_uri]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:feature_uri])
task_uri = OpenTox::Task.as_task("Mine features", url_for('/fminer',:full)) do
feature_dataset = OpenTox::Dataset.new
title = "BBRC representatives for " + training_dataset.title
feature_dataset.title = title
feature_dataset.creator = url_for('/fminer',:full)
bbrc_uri = url_for("/fminer#BBRC_representative",:full)
feature_dataset.features << bbrc_uri
id = 1 # fminer start id is not 0
compounds = []
g_hash = Hash.new# DV: for effect calculation in regression part
@@fminer.Reset
#@@fminer.SetChisqSig(0.99)
LOGGER.debug "Fminer: initialising ..."
training_dataset.data.each do |c,features|
begin
smiles = OpenTox::Compound.new(:uri => c.to_s).smiles
rescue
LOGGER.warn "No resource for #{c.to_s}"
next
end
if smiles == '' or smiles.nil?
LOGGER.warn "Cannot find smiles for #{c.to_s}."
else
feature_dataset.compounds << c.to_s
features.each do |feature|
act = feature[feature_uri]
if act.nil?
LOGGER.warn "No #{feature_uri} activiity for #{c.to_s}."
else
case act.to_s
when "true"
#LOGGER.debug id.to_s + ' "' + smiles +'"' + "\t" + true.to_s
activity = 1
when "false"
#LOGGER.debug id.to_s + ' "' + smiles +'"' + "\t" + false.to_s
activity = 0
else
# AM: add quantitative activity
activity = act.to_f
@@fminer.SetRegression(true)
end
compounds[id] = c.to_s
begin
@@fminer.AddCompound(smiles,id)
@@fminer.AddActivity(activity, id)
g_hash[id]=activity # DV: insert global information
rescue
LOGGER.warn "Could not add " + smiles + "\t" + act.to_s + " to fminer"
end
end
end
id += 1
end
end
g_array=g_hash.values # DV: calculation of global median for effect calculation
g_median=OpenTox::Utils.median(g_array)
minfreq = (0.02*id).round
@@fminer.SetMinfreq(minfreq)
LOGGER.debug "Fminer: initialised with #{id} compounds, minimum frequency #{minfreq}"
raise "no compounds" if compounds.size==0
values = {}
# run @@fminer
LOGGER.debug "Fminer: mining ..."
(0 .. @@fminer.GetNoRootNodes()-1).each do |j|
results = @@fminer.MineRoot(j)
results.each do |result|
f = YAML.load(result)[0]
smarts = f[0]
p_value = f[1]
# AM: f[3] missing on regression
if (!@@fminer.GetRegression)
ids = f[2] + f[3]
if f[2].size > f[3].size
effect = 'activating'
else
effect = 'deactivating'
end
else #regression part
ids = f[2]
# DV: effect calculation
f_arr=Array.new
f[2].each do |id|
f_arr.push(g_hash[id])
end
f_median=OpenTox::Utils.median(f_arr)
if g_median >= f_median
effect = 'activating'
else
effect = 'deactivating'
end
end
tuple = {
url_for('/fminer#smarts',:full) => smarts,
url_for('/fminer#p_value',:full) => p_value.to_f,
url_for('/fminer#effect',:full) => effect
}
#LOGGER.debug "#{f[0]}\t#{f[1]}\t#{effect}"
ids.each do |id|
feature_dataset.data[compounds[id]] = [] unless feature_dataset.data[compounds[id]]
feature_dataset.data[compounds[id]] << {bbrc_uri => tuple}
end
end
end
uri = feature_dataset.save
LOGGER.debug "Fminer finished, dataset #{uri} created."
uri
end
LOGGER.debug "Fimer task started: "+task_uri.to_s
response['Content-Type'] = 'text/uri-list'
halt 202,task_uri.to_s+"\n"
end
|
