code cleanup and refactoring.

1 files changed, 14 insertions, 339 deletions

diff --git a/application.rb b/application.rb
index dfdc952..20fadad 100644
--- a/application.rb
+++ b/application.rb
@@ -4,325 +4,27 @@
 
 require 'roo'
 require 'opentox-server'
-require './compound.rb'
+require_relative 'helper.rb'
+require_relative 'compound.rb'
+# TODO: remove and find a better way to test task errors
+require_relative 'test.rb'
 
 # Library code
 $logger.debug "Dataset booting: #{$dataset.collect{|k,v| "#{k}: '#{v}'"} }"
-Dir['./lib/compound/*.rb'].each { |f| require f; also_reload f } # Libs
-Dir['./lib/*.rb'].each { |f| require f; also_reload f } # Libs
-Dir['./webapp/*.rb'].each { |f| require f; also_reload f } # Webapps
 
-#require 'profiler'
+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
-
-        @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." # be careful with double quotes in literals!
-            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")
-      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
-      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
+    before do
+      #Profiler__::start_profile
+    end
 
-      def parse_put
-        task = OpenTox::Task.create $task[:uri], nil, RDF::DC.description => "Dataset upload: #{@uri}" do
-          #Profiler__::start_profile
-          case @content_type
-          when "text/plain", "text/turtle", "application/rdf+xml" # no conversion needed
-          when "text/csv"
-            @body = from_csv @body
-            @content_type = "text/plain"
-          when "application/vnd.ms-excel"
-            from_spreadsheet Excel
-          when "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
-            from_spreadsheet Excelx
-          when "application/vnd.oasis.opendocument.spreadsheet"
-            from_spreadsheet Openoffice
-    #      when "chemical/x-mdl-sdfile"
-    #        @body = parse_sdf @body
-    #        @content_type = "text/plain"
-          else
-            bad_request_error "#{@content_type} is not a supported content type."
-          end
-          #puts @body
-          FourStore.put @uri, @body, @content_type
-          if params[:file]
-            nt = "<#{@uri}> <#{RDF::DC.title}> \"#{params[:file][:filename]}\".\n<#{uri}> <#{RDF::OT.hasSource}> \"#{params[:file][:filename]}\"."
-            FourStore.post(@uri, nt, "text/plain")
-          end
-          #Profiler__::stop_profile
-          #Profiler__::print_profile($stdout)
-          @uri
-        end
-        response['Content-Type'] = "text/uri-list"
-        halt 202, task.uri
-      end
+    after do
+      #Profiler__::stop_profile
+      #Profiler__::print_profile($stdout)
     end
 
     before "/#{SERVICE}/:id/:property" do
@@ -336,7 +38,6 @@ module OpenTox
     end
 
     get "/dataset/:id/?" do
-      #Profiler__::start_profile
       case @accept
       when "application/rdf+xml", "text/turtle", "text/plain", /html/
         r = FourStore.get(@uri, @accept)
@@ -355,8 +56,6 @@ module OpenTox
           bad_request_error "'#{@accept}' is not a supported content type."
         end
       end
-      #Profiler__::stop_profile
-      #Profiler__::print_profile($stdout)
       r
     end
 
@@ -371,11 +70,9 @@ module OpenTox
       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.} 
+          { ?s ?p ?o.  <#{@uri}> ?p ?o. } UNION
+          { ?s ?p ?o. ?s <#{RDF.type}> <#{RDF::OT.Parameter}> . }
+          FILTER (?p != <#{RDF::OT.dataEntry}>)
         } "
         FourStore.query sparql, @accept
       else
@@ -413,28 +110,6 @@ module OpenTox
       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