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# Author: Christoph Helma, Andreas Maunz
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 = { Roo::Excel => ".xls", Roo::Excelx => ".xlsx", Roo::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
data = {}
data["warnings"] = []
data["type"] = ["Dataset","OrderedDataset"]
data["date"] = DateTime.now.to_s
data["data_entries"] = []
# features
feature_names = table.shift.collect{|f| f.strip}
data["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
data["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 = {"title" => f}
if values.size == 0 # empty feature
elsif values.size <= 5 # max classes
metadata["type"] = [ "NominalFeature", "StringFeature", "Feature" ]
metadata["acceptValue"] = values
end
if types.size == 1 and types[0] == "NumericFeature"
metadata["type"] ||= []
metadata["type"] << ["NumericFeature", "Feature"]
else
metadata["type"] = [ "NominalFeature", "StringFeature", "Feature" ] # only nominal type for mixed cases
metadata["acceptValue"] = values
end
feature = OpenTox::Feature.find_or_create metadata
data["features"] << feature.uri unless feature.nil?
end
# compounds and values
data["compounds"] = []
r = -1
table.each_with_index do |values,j|
compound = values.shift
compound_uri = nil
begin
case compound_format
when /URI|URL/i
compound_uri = compound
when /SMILES/i
c = OpenTox::Compound.from_smiles(compound)
if c.inchi.empty?
data["warnings"] << "Cannot parse #{compound_format} compound '#{compound}' at position #{j+2}, all entries are ignored."
next
else
compound_uri = c.uri
end
when /InChI/i
c = OpenTox::Compound.from_inchi(compound)
if c.inchi.empty?
data["warnings"] << "Cannot parse #{compound_format} compound '#{compound}' at position #{j+2}, all entries are ignored."
next
else
compound_uri = c.uri
end
else
raise "wrong compound format" #should be checked above
end
rescue
data["warnings"] << "Cannot parse #{compound_format} compound '#{compound}' at position #{j+2}, all entries are ignored." # be careful with double quotes in literals! \C in smiles is an illegal Turtle string
next
end
r += 1
data["compounds"] << compound_uri
unless values.size == data["features"].size
data["warnings"] << "Number of values at position #{j+2} (#{values.size}) is different than header size (#{features.size}), all entries are ignored."
next
end
# TODO ordering/index
#data_entry_node = "<#{File.join @uri,"dataentry",j.to_s}>" # too slow or not accepted by 4store
data["data_entries"] << values
values.each_with_index do |v,i|
if v.blank?
data["warnings"] << "Empty value for compound '#{compound}' (row #{r+2}) and feature '#{feature_names[i]}' (column #{i+2})."
next
end
end
end
data["compounds"].duplicates.each do |uri|
positions = []
data["compounds"].each_with_index{|c,i| positions << i+1 if !c.blank? and c == uri}
data["warnings"] << "Duplicate compound #{uri} at rows #{positions.join(', ')}. Entries are accepted, assuming that measurements come from independent experiments."
end
data
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
#to_table
end
def to_table
# TODO: fix and speed up
sparql = "SELECT DISTINCT ?s FROM <#{@uri}> WHERE {
?s <#{RDF.type}> <#{RDF::OT.Feature}> ;
<#{RDF::OLO.index}> ?fidx
} ORDER BY ?fidx"
features = FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| OpenTox::Feature.new uri }
sparql = "SELECT DISTINCT ?compound FROM <#{@uri}> WHERE {
?compound <#{RDF.type}> <#{RDF::OT.Compound}> ;
<#{RDF::OLO.index}> ?cidx;
} ORDER BY ?cidx"
inchis = FourStore.query(sparql, "text/uri-list").split("\n").collect { |uri| "InChI#{uri.split("InChI").last}" }
table = [["InChI"] + features.collect{|f| f.title}]
inchis.each{|inchi| table << [inchi]}
sparql = "SELECT ?cidx ?fidx ?value FROM <#{@uri}> WHERE {
?data_entry <#{RDF::OLO.index}> ?cidx ;
<#{RDF::OT.values}> ?v .
?v <#{RDF::OT.feature}> ?f;
<#{RDF::OT.value}> ?value .
?f <#{RDF::OLO.index}> ?fidx.
} ORDER BY ?fidx ?cidx"
FourStore.query(sparql,"text/uri-list").split("\n").each do |row|
r,c,v = row.split("\t")
table[r.to_i+1][c.to_i+1] = v.to_s
end
table
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.run "Dataset upload", @uri do
case @content_type
when "application/json" # no conversion needed
#when "text/plain", "text/turtle", "application/rdf+xml" # no conversion needed
when "text/csv", "text/comma-separated-values"
@body = from_csv @body
# 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
if params["file"]
@body[:title] = params["file"][:filename]
@body[:hasSource] = params["file"][:filename]
end
@body["uri"] = @uri
@body["uuid"] = @uri.split(/\//).last
$mongo[SERVICE].insert_one(@body).inspect
@uri
end
response['Content-Type'] = "text/uri-list"
halt 202, task.uri
end
end
end
end
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