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# dataset.rb
# Loads libraries and webapps
# Author: Christoph Helma, Andreas Maunz
require 'roo'
require 'opentox-server'
require './compound.rb'
# Library code
$logger.debug "Dataset booting: #{$dataset.collect{|k,v| "#{k}: '#{v}'"} }"
Dir['./lib/compound/*.rb'].each { |f| require f } # Libs
Dir['./lib/*.rb'].each { |f| require f } # Libs
Dir['./webapp/*.rb'].each { |f| require f } # Webapps
#require 'profiler'
# Entry point
module OpenTox
class Application < Service
@warnings = []
helpers do
def from_csv(csv)
table = CSV.parse(csv)
# CSVs with unexpected encodings may have blanks instead of nil
table.collect! { |row|
row.collect! { |val|
(val.class == String and val.strip == "") ? nil : val
}
}
from_table table
end
def from_spreadsheet spreadsheet
extensions = { Excel => ".xls", Excelx => ".xlsx", Openoffice => ".ods" }
input = params[:file][:tempfile].path + ".xls"
csv_file = params[:file][:tempfile].path + ".csv"
File.rename params[:file][:tempfile].path, input # roo needs "correct" extensions
spreadsheet.new(input).to_csv csv_file # roo cannot write to strings
@body = from_csv File.read(csv_file)
@content_type = "text/plain"
end
=begin
def from_sdf(sdf)
#obconversion = OpenBabel::OBConversion.new
#obmol = OpenBabel::OBMol.new
#obconversion.set_in_and_out_formats "sdf", "inchi"
table = []
properties = []
sdf.each_line { |l| properties << l.to_s if l.match(/</) }
properties.sort!
properties.uniq!
properties.collect!{ |p| p.gsub(/<|>/,'').strip.chomp }
properties.insert 0, "InChI"
table[0] = properties
rec = 0
sdf.split(/\$\$\$\$\r*\n/).each do |s|
rec += 1
table << []
begin
# TODO: use compound service
compound = OpenTox::Compound.from_sdf sdf
#obconversion.read_string obmol, s
table.last << obconversion.write_string(obmol).gsub(/\s/,'').chomp
rescue
# TODO: Fix, will lead to follow up errors
table.last << "Could not convert structure at record #{rec}) have been ignored! \n#{s}"
end
obmol.get_data.each { |d| table.last[table.first.index(d.get_attribute)] = d.get_value }
end
from_table table
end
=end
def from_table table
=begin
dataset = OpenTox::Dataset.new @uri
puts dataset.uri
feature_names = table.shift.collect{|f| f.strip}
puts feature_names.inspect
dataset.append RDF::OT.Warnings, "Duplicate features in table header." unless feature_names.size == feature_names.uniq.size
compound_format = feature_names.shift.strip
bad_request_error "#{compound_format} is not a supported compound format. Accepted formats: URI, SMILES, InChI." unless compound_format =~ /URI|URL|SMILES|InChI/i
features = []
feature_names.each_with_index do |f,i|
feature = OpenTox::Feature.new File.join($feature[:uri], SecureRandom.uuid)
feature[RDF::DC.title] = f
features << feature
values = table.collect{|row| row[i+1].strip unless row[i+1].nil?}.uniq.compact # skip compound column
if values.size <= 3 # max classes
feature.append RDF.type, RDF::OT.NominalFeature
feature.append RDF.type, RDF::OT.StringFeature
feature[RDF::OT.acceptValue] = values
else
types = values.collect{|v| feature_type(v)}
if types.include?(RDF::OT.NominalFeature)
dataset.append RDF::OT.Warnings, "Feature #{f} contains nominal and numeric values."
else
feature.append RDF.type, RDF::OT.NumericFeature
end
end
feature.put
end
dataset.features = features
compounds = []
table.each_with_index do |values,j|
c = values.shift
puts c
puts compound_format
values.collect!{|v| v.nil? ? nil : v.strip }
#begin
case compound_format
when /URI|URL/i
compound = OpenTox::Compound.new c
when /SMILES/i
compound = OpenTox::Compound.from_smiles($compound[:uri], c)
when /InChI/i
compound = OpenTox::Compound.from_inchi($compound[:uri], URI.decode_www_form_component(c))
end
#rescue
#dataset.append RDF::OT.Warnings, "Cannot parse compound \"#{c}\" at position #{j+2}, all entries are ignored."
#next
#end
unless compound_uri.match(/InChI=/)
dataset.append RDF::OT.Warnings, "Cannot parse compound \"#{c}\" at position #{j+2}, all entries are ignored."
next
end
compounds << compound
unless values.size == features.size
dataset.append RDF::OT.Warnings, "Number of values at position #{j+2} (#{values.size}) is different than header size (#{features.size}), all entries are ignored."
next
end
dataset << values
end
dataset.compounds = compounds
compounds.duplicates.each do |compound|
positions = []
compounds.each_with_index{|c,i| positions << i+1 if c.uri == compound.uri}
dataset.append RDF::OT.Warnings, "Duplicate compound #{compound.uri} at rows #{positions.join(', ')}. Entries are accepted, assuming that measurements come from independent experiments."
end
puts dataset.to_ntriples
dataset.to_ntriples
=end
begin
@warnings = []
ntriples = ["<#{@uri}> <#{RDF.type}> <#{RDF::OT.Dataset}>."]
ntriples << ["<#{@uri}> <#{RDF.type}> <#{RDF::OT.OrderedDataset}>."]
# features
feature_names = table.shift.collect{|f| f.strip}
@warnings << "Duplicate features in table header." unless feature_names.size == feature_names.uniq.size
compound_format = feature_names.shift.strip
bad_request_error "#{compound_format} is not a supported compound format. Accepted formats: URI, SMILES, InChI." unless compound_format =~ /URI|URL|SMILES|InChI/i
features = []
ignored_feature_indices = []
feature_names.each_with_index do |f,i|
values = table.collect{|row| val=row[i+1]; val.strip! unless val.nil?; val }.uniq.compact
types = values.collect{|v| feature_type(v)}.uniq
metadata = {}
if values.size == 0 # empty feature
elsif values.size <= 5 # max classes
metadata[RDF.type] = [ RDF::OT.NominalFeature, RDF::OT.StringFeature ]
metadata[RDF::OT.acceptValue] = values
end
if types.size == 1 and types[0] == RDF::OT.NumericFeature
metadata[RDF.type] = [] unless metadata[RDF.type]
metadata[RDF.type] << RDF::OT.NumericFeature
else
metadata[RDF.type] = [ RDF::OT.NominalFeature, RDF::OT.StringFeature ] # only nominal type for mixed cases
metadata[RDF::OT.acceptValue] = values
end
feature = OpenTox::Feature.find_by_title(f,metadata) # AM: find or generate
features << feature unless feature.nil?
ntriples << "<#{feature.uri}> <#{RDF.type}> <#{RDF::OT.Feature}>."
ntriples << "<#{feature.uri}> <#{RDF::OLO.index}> #{i} ."
end
# compounds and values
compound_uris = []
table.each_with_index do |values,j|
compound = values.shift
begin
case compound_format
when /URI|URL/i
compound_uri = compound
when /SMILES/i
compound_uri = OpenTox::Compound.from_smiles($compound[:uri], compound).uri
when /InChI/i
compound_uri = OpenTox::Compound.from_inchi($compound[:uri], compound).uri
end
rescue
@warnings << "Cannot parse compound \"#{compound}\" at position #{j+2}, all entries are ignored."
next
end
unless compound_uri.match(/InChI=/)
@warnings << "Cannot parse compound \"#{compound}\" at position #{j+2}, all entries are ignored."
next
end
compound_uris << compound_uri
unless values.size == features.size
@warnings << "Number of values at position #{j+2} (#{values.size}) is different than header size (#{features.size}), all entries are ignored."
next
end
ntriples << "<#{compound_uri}> <#{RDF.type}> <#{RDF::OT.Compound}>."
ntriples << "<#{compound_uri}> <#{RDF::OLO.index}> #{j} ."
values.each_with_index do |v,i|
#@warnings << "Empty value for compound #{compound} (row #{j+2}) and feature \"#{feature_names[i]}\" (column #{i+2})." if v.blank?
#@warnings << "Empty value in row #{j+2}, column #{i+2} (feature \"#{feature_names[i]}\")." if v.blank?
data_entry_node = "_:dataentry"+ j.to_s
value_node = data_entry_node+ "_value"+ i.to_s
ntriples << "<#{@uri}> <#{RDF::OT.dataEntry}> #{data_entry_node} ."
ntriples << "#{data_entry_node} <#{RDF.type}> <#{RDF::OT.DataEntry}> ."
ntriples << "#{data_entry_node} <#{RDF::OLO.index}> #{j} ."
ntriples << "#{data_entry_node} <#{RDF::OT.compound}> <#{compound_uri}> ."
ntriples << "#{data_entry_node} <#{RDF::OT.values}> #{value_node} ."
ntriples << "#{value_node} <#{RDF::OT.feature}> <#{features[i].uri}> ."
ntriples << "#{value_node} <#{RDF::OT.value}> \"#{v}\" ."
end
end
compound_uris.duplicates.each do |uri|
positions = []
compound_uris.each_with_index{|c,i| positions << i+1 if c == uri}
@warnings << "Duplicate compound #{uri} at rows #{positions.join(', ')}. Entries are accepted, assuming that measurements come from independent experiments."
end
ntriples << "<#{@uri}> <#{RDF::OT.Warnings}> \"#{@warnings.join('\n')}\" ."
ntriples.join("\n")
rescue Exception => e
$logger.debug "#{e.class}: #{e.message}"
$logger.debug "Backtrace:\n\t#{e.backtrace.join("\n\t")}"
end
=begin
=end
end
=begin
def to_xlsx
# both simple_xlsx and axlsx create empty documents with OLE2 errors
xlsx = @uri.split("/").last+".xlsx"
p = Axlsx::Package.new
wb = p.workbook
wb.add_worksheet(:name => "test") do |sheet|
to_table.each { |row| sheet.add_row row; puts row }
end
p.serialize("test.xlsx")
p.to_stream
#```
#Tempfile.open(@uri.split("/").last+".xlsx") do |xlsx|
SimpleXlsx::Serializer.new(xlsx) do |doc|
doc.add_sheet("People") do |sheet|
to_table.each { |row| sheet.add_row row }
end
end
send_file xlsx
#end
end
=end
def to_csv
csv_string = CSV.generate do |csv|
to_table.each { |row| csv << row }
end
csv_string.gsub(/\"\"/,"") # AM: no quotes for missing values
end
def to_table
=begin
table = []
dataset = OpenTox::Dataset.new @uri
dataset.get
table << ["SMILES"] + dataset.features.collect{|f| f.get; f.title}
dataset.data_entries.each_with_index do |data_entry,i|
table << [dataset.compounds[i]] + data_entry
end
table
=end
accept = "text/uri-list"
table = []
if ordered?
features = OpenTox::Dataset.find_features_sparql(@uri)
sparql_constraints = {:type => RDF.type, :title => RDF::DC.title}
feature_props = OpenTox::Dataset.find_props_sparql(features.collect { |f| f.uri }, sparql_constraints)
quoted_features = []; feature_names = []
features.each { |feature|
quoted_features << feature_props[feature.uri][:type].include?(RDF::OT.NominalFeature)
feature_names << "\"#{feature_props[feature.uri][:title][0].strip}\""
}
compounds = OpenTox::Dataset.find_compounds_sparql(@uri)
values = OpenTox::Dataset.find_data_entries_sparql(@uri)
values += Array.new(compounds.size*features.size-values.size, "")
clim=(compounds.size-1)
cidx = fidx = 0
num=(!quoted_features[fidx])
table = (Array.new((features.size)*(compounds.size))).each_slice(features.size).to_a
values.each { |val|
unless val.blank?
table[cidx][fidx] = (num ? val : "\"#{val}\"")
end
if (cidx < clim)
cidx+=1
else
cidx=0
fidx+=1
num=(!quoted_features[fidx])
end
}
table.each_with_index { |row,idx| row.unshift("\"#{compounds[idx].inchi}\"") }
table.unshift([ "\"InChI\"" ] + feature_names)
else
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Feature}>}"
features = FourStore.query(sparql, accept).split("\n").collect{|uri| OpenTox::Feature.new uri}.each { |f| f.get }
quoted_features = features.each_with_index.collect { |f,idx|
if (f[RDF.type].include?(RDF::OT.NominalFeature) or
f[RDF.type].include?(RDF::OT.StringFeature) and
!f[RDF.type].include?(RDF::OT.NumericFeature))
idx+1
end
}.compact
table << ["InChI"] + features.collect{ |f| "\"" + f[RDF::DC.title] + "\"" }
sparql = "SELECT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Compound}>. }"
compounds = FourStore.query(sparql, accept).split("\n").collect{|uri| OpenTox::Compound.new uri}
compounds.each do |compound|
data_entries = []
features.each do |feature|
sparql = "SELECT ?value FROM <#{@uri}> WHERE {
?data_entry <#{RDF::OT.compound}> <#{compound.uri}>;
<#{RDF::OT.values}> ?v .
?v <#{RDF::OT.feature}> <#{feature.uri}>;
<#{RDF::OT.value}> ?value.
} ORDER BY ?data_entry"
FourStore.query(sparql, accept).split("\n").each do |value|
data_entries << value
end
end
row = ["\"#{compound.inchi}\""] + data_entries
row = row.each_with_index.collect { |value,idx| (quoted_features.include?(idx) ? "\"#{value}\"" : value) }
table << row
end
end
table
=begin
=end
end
def feature_type(value)
if value.blank?
nil
elsif value.numeric?
RDF::OT.NumericFeature
else
RDF::OT.NominalFeature
end
end
def ordered?
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.OrderedDataset}>}"
FourStore.query(sparql, "text/uri-list").split("\n").empty? ? false : true
end
def parse_put
task = OpenTox::Task.create $task[:uri], nil, RDF::DC.description => "Dataset upload: #{@uri}" do
#Profiler__::start_profile
case @content_type
when "text/plain", "text/turtle", "application/rdf+xml" # no conversion needed
when "text/csv"
@body = from_csv @body
@content_type = "text/plain"
when "application/vnd.ms-excel"
from_spreadsheet Excel
when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
from_spreadsheet Excelx
when "application/vnd.oasis.opendocument.spreadsheet"
from_spreadsheet Openoffice
# when "chemical/x-mdl-sdfile"
# @body = parse_sdf @body
# @content_type = "text/plain"
else
bad_request_error "#{@content_type} is not a supported content type."
end
FourStore.put @uri, @body, @content_type
if params[:file]
nt = "<#{@uri}> <#{RDF::DC.title}> \"#{params[:file][:filename]}\".\n<#{uri}> <#{RDF::OT.hasSource}> \"#{params[:file][:filename]}\"."
FourStore.post(@uri, nt, "text/plain")
end
#Profiler__::stop_profile
#Profiler__::print_profile($stdout)
@uri
end
response['Content-Type'] = "text/uri-list"
halt 202, task.uri
end
end
before "/#{SERVICE}/:id/:property" do
@uri = uri("/#{SERVICE}/#{params[:id]}")
end
# Create a new resource
post "/dataset/?" do
@uri = uri("/#{SERVICE}/#{SecureRandom.uuid}")
parse_put
end
get "/dataset/:id/?" do
#Profiler__::start_profile
case @accept
when "application/rdf+xml", "text/turtle", "text/plain", /html/
r = FourStore.get(@uri, @accept)
else
case @accept
when "text/csv"
r = to_csv
#when "application/vnd.ms-excel"
#to_spreadsheet Excel
#when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
#to_xlsx
#when "application/vnd.oasis.opendocument.spreadsheet"
#to_spreadsheet Openoffice
#when "chemical/x-mdl-sdfile"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
end
#Profiler__::stop_profile
#Profiler__::print_profile($stdout)
r
end
# Create or update a resource
put "/dataset/:id/?" do
parse_put
end
# Get metadata of the dataset
# @return [application/rdf+xml] Metadata OWL-DL
get '/dataset/:id/metadata' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {
{ ?s ?p ?o. <#{@uri}> <#{RDF.type}> ?o. } UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::DC.title}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::DC.creator}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::OT.Warnings}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::OT.hasSource}> ?o.}
} "
FourStore.query sparql, @accept
else
bad_request_error "'#{@accept}' is not a supported content type."
end
end
# Get a list of all features
# @param [Header] Accept one of `application/rdf+xml, text/turtle, text/plain, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, text/turtle, text/plain, text/uri-list] Feature data
get '/dataset/:id/features' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Feature}>; ?p ?o. }"
when "text/uri-list"
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Feature}>. ?s <#{RDF::OLO.index}> ?idx } ORDER BY ?idx"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
FourStore.query sparql, @accept
end
# Get a list of all compounds
# @param [Header] Accept one of `application/rdf+xml, text/turtle, text/plain, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, text/turtle, text/plain, text/uri-list] Compound data
get '/dataset/:id/compounds' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Compound}>; ?p ?o. }"
when "text/uri-list"
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {?s <#{RDF.type}> <#{RDF::OT.Compound}>. ?s <#{RDF::OLO.index}> ?idx } ORDER BY ?idx"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
FourStore.query sparql, @accept
end
# Get everything but the data entries
# @param [Header] Accept one of `application/rdf+xml, text/turtle, text/plain, text/uri-list` (default application/rdf+xml)
# @return [application/rdf+xml, text/turtle, text/plain, text/uri-list] The data
get '/dataset/:id/allnde' do
case @accept
when "application/rdf+xml", "text/turtle", "text/plain"
sparql = "CONSTRUCT {?s ?p ?o.} FROM <#{@uri}> WHERE {
{ ?s ?p ?o. <#{@uri}> <#{RDF.type}> ?o. } UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::DC.title}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::DC.creator}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::OT.Warnings}> ?o.} UNION
{ ?s ?p ?o. <#{@uri}> <#{RDF::OT.hasSource}> ?o.} UNION
{ ?s ?p ?o. ?s <#{RDF.type}> <#{RDF::OT.Feature}> } UNION
{ ?s ?p ?o. ?s <#{RDF.type}> <#{RDF::OT.Parameter}> }
}"
else
bad_request_error "'#{@accept}' is not a supported content type."
end
FourStore.query sparql, @accept
end
end
end
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