diff options
Diffstat (limited to 'lib')
| -rw-r--r-- | lib/compound.rb | 26 | ||||
| -rw-r--r-- | lib/opentox.rb | 4 | ||||
| -rw-r--r-- | lib/overwrite.rb | 16 |
3 files changed, 22 insertions, 24 deletions
diff --git a/lib/compound.rb b/lib/compound.rb index 51ef96d..89bf840 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -175,19 +175,18 @@ module OpenTox end # Convert identifier from OpenBabel input_format to OpenBabel output_format - def self.obconversion(identifier,input_format,output_format) - obconversion = OpenBabel::OBConversion.new - obmol = OpenBabel::OBMol.new - obconversion.set_in_and_out_formats input_format, output_format - obconversion.read_string obmol, identifier - case output_format - when /smi|can|inchi/ - obconversion.write_string(obmol).gsub(/\s/,'').chomp - else - obconversion.write_string(obmol) - end - end -=end + def self.obconversion(identifier,input_format,output_format) + obconversion = OpenBabel::OBConversion.new + obmol = OpenBabel::OBMol.new + obconversion.set_in_and_out_formats input_format, output_format + obconversion.read_string obmol, identifier + case output_format + when /smi|can|inchi/ + obconversion.write_string(obmol).gsub(/\s/,'').chomp + else + obconversion.write_string(obmol) + end + end @@ -225,6 +224,7 @@ module OpenTox def match(smarts_array) match_hits(smarts_array,false) end +=end end end diff --git a/lib/opentox.rb b/lib/opentox.rb index 09e5e41..95dca04 100644 --- a/lib/opentox.rb +++ b/lib/opentox.rb @@ -108,6 +108,8 @@ module OpenTox # Save object at webservice (replace or create object) def put wait=true, mime_type="text/plain" bad_request_error "Mime type #{mime_type} is not supported. Please use 'text/plain' (default) or 'application/rdf+xml'." unless mime_type == "text/plain" or mime_type == "application/rdf+xml" + @metadata[RDF::OT.created_at] = DateTime.now unless URI.accessible? @uri, @subjectid + #@metadata[RDF::DC.modified] = DateTime.now case mime_type when 'text/plain' body = self.to_ntriples @@ -129,7 +131,7 @@ module OpenTox end def create_rdf - @rdf = RDF::Graph.new if @rdf.empty? or URI.task?(@uri) + @rdf = RDF::Graph.new #if @rdf.empty? or URI.task?(@uri) @metadata[RDF.type] ||= eval("RDF::OT."+self.class.to_s.split('::').last) @metadata[RDF::DC.date] ||= DateTime.now @metadata.each do |predicate,values| diff --git a/lib/overwrite.rb b/lib/overwrite.rb index fbe8f7d..04de58d 100644 --- a/lib/overwrite.rb +++ b/lib/overwrite.rb @@ -77,11 +77,11 @@ module URI end def self.dataset? uri, subjectid=nil - uri =~ /dataset/ and URI.accessible? uri, subjectid=nil + uri =~ /dataset/ and URI.accessible? uri, subjectid end def self.model? uri, subjectid=nil - uri =~ /model/ and URI.accessible? uri, subjectid=nil + uri =~ /model/ and URI.accessible? uri, subjectid end def self.ssl? uri, subjectid=nil @@ -92,17 +92,13 @@ module URI def self.accessible?(uri, subjectid=nil) parsed_uri = URI.parse(uri + (subjectid ? "?subjectid=#{CGI.escape subjectid}" : "")) http_code = URI.task?(uri) ? 600 : 400 - unless (URI.ssl? uri) == true - http = Net::HTTP.new(parsed_uri.host, parsed_uri.port) - request = Net::HTTP::Head.new(parsed_uri.request_uri) - http.request(request).code.to_i < http_code - else - http = Net::HTTP.new(parsed_uri.host, parsed_uri.port) + http = Net::HTTP.new(parsed_uri.host, parsed_uri.port) + if (URI.ssl? uri) == true http.use_ssl = true http.verify_mode = OpenSSL::SSL::VERIFY_NONE - request = Net::HTTP::Head.new(parsed_uri.request_uri) - http.request(request).code.to_i < http_code end + request = Net::HTTP::Head.new(parsed_uri.request_uri) + http.request(request).code.to_i < http_code rescue false end |