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# Get all datasets
get "/dataset/?" do
datasets = Dataset.all
case @accept
when "text/uri-list"
uri_list = datasets.collect{|dataset| uri("/dataset/#{dataset.id}")}
return uri_list.join("\n") + "\n"
when "application/json"
datasets = JSON.parse datasets.to_json
list = []
datasets.each{|d| list << uri("/dataset/#{d["_id"]["$oid"]}")}
return list.to_json
else
bad_request_error "Mime type #{@accept} is not supported."
end
end
# Get a dataset
get "/dataset/:id/?" do
if Task.where(id: params[:id]).exists?
task = Task.find params[:id]
halt 404, "Dataset with id: #{params[:id]} not found." unless task.percent == 100
$logger.debug task.inspect
response['Content-Type'] = "text/csv"
m = Model::Validation.find task.model_id
dataset = Batch.find task.dataset_id
@ids = dataset.ids
warnings = dataset.warnings.blank? ? nil : dataset.warnings.join("\n")
unless warnings.nil?
@parse = []
warnings.split("\n").each do |warning|
if warning =~ /^Cannot/
smi = warning.split("SMILES compound").last.split("at").first
line = warning.split("SMILES compound").last.split("at line").last.split("of").first.strip.to_i
@parse << "Cannot parse SMILES compound#{smi}at line #{line} of #{dataset.source.split("/").last}\n"
end
end
keys_array = []
warnings.split("\n").each do |warning|
if warning =~ /^Duplicate/
text = warning.split("ID").first
numbers = warning.split("ID").last.split("and")
keys_array << numbers.collect{|n| n.strip.to_i}
end
end
@dups = {}
keys_array.each do |keys|
keys.each do |key|
@dups[key] = "Duplicate compound at ID #{keys.join(" and ")}\n"
end
end
end
$logger.debug "dups: #{@dups}"
endpoint = "#{m.endpoint}_(#{m.species})"
tempfile = Tempfile.new
header = task.csv
lines = []
$logger.debug task.predictions
task.predictions[m.id.to_s].each_with_index do |hash,idx|
identifier = hash.keys[0]
prediction_id = hash.values[0]
# add duplicate warning at the end of a line if ID matches
if @dups[idx+1]
if prediction_id.is_a? BSON::ObjectId
if @ids.blank?
lines << "#{idx+1},#{identifier},#{Prediction.find(prediction_id).csv.tr("\n","")},#{@dups[idx+1]}"
else
lines << "#{idx+1},#{@ids[idx]},#{identifier},#{Prediction.find(prediction_id).csv.tr("\n","")},#{@dups[idx+1]}"
end
else
if @ids.blank?
lines << "#{idx+1},#{identifier},\n"
else
lines << "#{idx+1},#{@ids[idx]}#{identifier},\n"
end
end
else
if prediction_id.is_a? BSON::ObjectId
if @ids.blank?
lines << "#{idx+1},#{identifier},#{Prediction.find(prediction_id).csv}"
else
lines << "#{idx+1},#{@ids[idx]},#{identifier},#{Prediction.find(prediction_id).csv}"
end
else
if @ids.blank?
lines << "#{idx+1},#{identifier},\n"
else
lines << "#{idx+1},#{@ids[idx]}#{identifier},\n"
end
end
end
end
(@parse && !@parse.blank?) ? tempfile.write(header+lines.join("")+"\n"+@parse.join("\n")) : tempfile.write(header+lines.join(""))
#tempfile.write(header+lines.join(""))
tempfile.rewind
########################
=begin
header = task.csv
lines = []
task.predictions.each_with_index do |result,idx|
identifier = result[0]
prediction_id = result[1]
prediction = Prediction.find prediction_id
lines << "#{idx+1},#{identifier},#{prediction.csv.tr("\n","")}"
end
return header+lines.join("\n")
=end
return tempfile.read
else
dataset = Dataset.find :id => params[:id]
halt 400, "Dataset with id: #{params[:id]} not found." unless dataset
case @accept
when "application/json"
dataset.data_entries.each do |k, v|
dataset.data_entries[k][:URI] = uri("/substance/#{k}")
end
dataset[:URI] = uri("/dataset/#{dataset.id}")
dataset[:substances] = uri("/dataset/#{dataset.id}/substances")
dataset[:features] = uri("/dataset/#{dataset.id}/features")
return dataset.to_json
when "text/csv", "application/csv"
return dataset.to_csv
else
bad_request_error "Mime type #{@accept} is not supported."
end
end
end
# Get a dataset attribute. One of compounds, nanoparticles, substances, features
get "/dataset/:id/:attribute/?" do
if Task.where(id: params[:id]).exists?
halt 400, "No attributes selection available for dataset with id: #{params[:id]}.".to_json
end
dataset = Dataset.find :id => params[:id]
halt 400, "Dataset with id: #{params[:id]} not found." unless dataset
attribs = ["compounds", "nanoparticles", "substances", "features"]
return "Attribute '#{params[:attribute]}' is not available. Choose one of #{attribs.join(', ')}." unless attribs.include? params[:attribute]
out = dataset.send("#{params[:attribute]}")
return out.to_json
end
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