code cleanup and refactoring.

1 files changed, 347 insertions, 0 deletions

diff --git a/helper.rb b/helper.rb
new file mode 100644
index 0000000..c405963
--- /dev/null
+++ b/helper.rb
@@ -0,0 +1,347 @@
+# 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 = { 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
+
+        @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 = {RDF::DC.title => f}
+          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_or_create metadata, @subjectid # 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
+            when /InChI/i
+              compound_uri = OpenTox::Compound.from_inchi(compound).uri
+            end
+          rescue
+            @warnings << "Cannot parse 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
+          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?
+
+            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")
+      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
+        #to_table
+      end
+
+      def compound_uris
+      end
+
+      def features
+      end
+
+      def data_entries
+      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#.inspect
+=begin
+        table = []
+        dataset = OpenTox::Dataset.new @uri
+        table << ["SMILES"] + dataset.features.collect{|f| f.title}
+        dataset.data_entries.each_with_index do |data_entry,i|
+          table << [dataset.compounds[i]] + data_entry
+        end
+        table
+=end
+=begin
+        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
+=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.run "Dataset upload", @uri, @subjectid do
+          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
+          if params["file"]
+            nt = "<#{@uri}> <#{RDF::DC.title}> \"#{params["file"][:filename]}\".\n<#{uri}> <#{RDF::OT.hasSource}> \"#{params["file"][:filename]}\"."
+            FourStore.put(@uri, nt, "text/plain")
+          end
+          nt ? FourStore.post(@uri, @body, @content_type) : FourStore.put(@uri, @body, @content_type) 
+          @uri
+        end
+        response['Content-Type'] = "text/uri-list"
+        halt 202, task.uri
+      end
+    end
+
+  end
+end
+