Merged shims

author: Andreas Maunz <andreas@maunz.de> 2012-10-24 16:35:31 +0200
committer: Andreas Maunz <andreas@maunz.de> 2012-10-24 16:35:31 +0200
commit: ad1725a4ee950b15d9d7c5d10a56babd0ae3706a (patch)
tree: f760ee460f2fd16022970013e4d75e9263977169
parent: 9b86169dfb87e60c81ae4dd55312cdb5b1b9d2e9 (diff)
4 files changed, 2 insertions, 188 deletions
diff --git a/application.rb b/application.rb
index 7c3d766..434555a 100644
--- a/application.rb
+++ b/application.rb
@@ -2,6 +2,8 @@
 # Loads libraries and webapps
 # Author: Christoph Helma, Andreas Maunz
 
+require 'sinatra/url_for'
+
 # Library code
 $logger.debug "Compound booting: #{$compound.collect{|k,v| "#{k}: '#{v}'"} }"
 Dir['./lib/utils/shims/*.rb'].each { |f| require f } # Shims for legacy code
diff --git a/lib/utils/html.rb b/lib/utils/html.rb
deleted file mode 100644
index 0392a1d..0000000
--- a/lib/utils/html.rb
+++ /dev/null
@@ -1,50 +0,0 @@
-#OT_LOGO = File.join(CONFIG[:services]["opentox-validation"],"resources/ot-logo.png")
-
-=begin
-* Name: html.rb
-* Description: Tools to provide html output
-* Author: Andreas Maunz <andreas@maunz.de>
-* Date: 10/2012
-=end
-
-# AM: needed since this gem has a nested directory structure
-require 'sinatra/url_for'
-
-class String
-  # encloses URI in text with with link tag
-  # @return [String] new text with marked links
-  def link_urls
-    regex = Regexp.new '(https?:\/\/[\S]+)([>"])'
-    self.gsub( regex, '<a href="\1">\1</a>\2' )
-  end
-end
-
-module OpenTox
-  
-  # produces a html page for making web services browser friendly
-  # format of text (=string params) is preserved (e.g. line breaks)
-  # urls are marked as links
-  #
-  # @param [String] text this is the actual content, 
-  # @param [optional,String] related_links info on related resources
-  # @param [optional,String] description general info
-  # @param [optional,Array] post_command, infos for the post operation, object defined below
-  # @return [String] html page
-  def self.text_to_html( text, subjectid=nil, related_links=nil, description=nil, post_command=nil  )
-    
-    # TODO add title as parameter
-    title = nil #$sinatra.url_for($sinatra.request.env['PATH_INFO'], :full) if $sinatra
-    html = "<html>"
-    html += "<title>"+title+"</title>" if title
-    #html += "<img src=\""+OT_LOGO+"\"><\/img><body>"
-      
-    html += "<h3>Description</h3><pre><p>"+description.link_urls+"</p></pre>" if description
-    html += "<h3>Related links</h3><pre><p>"+related_links.link_urls+"</p></pre>" if related_links
-    html += "<h3>Content</h3>" if description || related_links
-    html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
-    html += text.link_urls
-    html += "</p></pre></body></html>"
-    html
-  end
-  
-end
diff --git a/lib/utils/shims/feature.rb b/lib/utils/shims/feature.rb
deleted file mode 100644
index 297748b..0000000
--- a/lib/utils/shims/feature.rb
+++ /dev/null
@@ -1,87 +0,0 @@
-=begin
-* Name: feature.rb
-* Description: Feature shims
-* Author: Andreas Maunz <andreas@maunz.de>
-* Date: 10/2012
-=end
-
-module OpenTox
-
-  # Shims for the feature class
-  class Feature
-
-    # Load a feature from URI
-    # @param [String] Feature URI
-    # @return [OpenTox::Feature] Feature object with the full data
-    def self.find(uri, subjectid=nil)
-      return nil unless uri
-      f = OpenTox::Feature.new uri, subjectid
-      f.get
-      f
-    end
-
-    # Load or create a feature given its title and metadata
-    # Create it if: a) not present, or b) present, but differs in metadata
-    # Newly created features are stored at the backend
-    # @param[String] title Feature title
-    # @param[Hash] metadata Feature metadata
-    # @return [OpenTox::Feature] Feature object with the full data, or nil
-    def self.find_by_title(title, metadata)
-      metadata[RDF.type] = [] unless metadata[RDF.type]
-      metadata[RDF.type] << RDF::OT.Feature unless metadata[RDF.type].include?(RDF::OT.Feature)
-      metadata[RDF::DC.title] = title unless (metadata[RDF::DC.title])
-      feature = feature_new = OpenTox::Feature.new File.join($feature[:uri], SecureRandom.uuid), @subjectid
-      feature_new.metadata = metadata
-      sparql = "SELECT DISTINCT ?feature WHERE { ?feature <#{RDF.type}> <#{RDF::OT['feature'.capitalize]}>. ?feature <#{RDF::DC.title}> '#{title.to_s}' }"
-      feature_uris = OpenTox::Backend::FourStore.query(sparql,"text/uri-list").split("\n")
-      features_equal = false # relevant also when no features found
-      feature_uris.each_with_index { |feature_uri,idx|
-        feature_existing = OpenTox::Feature.find(feature_uri, @subjectid)
-        if (feature_new.metadata.size+1 == feature_existing.metadata.size) # +1 due to title
-          features_equal = metadata.keys.collect { |predicate|
-            unless ( predicate == RDF::DC.title )
-              if feature_new[predicate].class == feature_existing[predicate].class
-                case feature_new[predicate].class.to_s
-                  when "Array" then (feature_new[predicate].sort == feature_existing[predicate].sort)
-                  else (feature_new[predicate] == feature_existing[predicate])
-                end
-              end
-            else
-              true
-            end
-          }.uniq == [true]
-        end
-        (feature=feature_existing and break) if features_equal
-      }
-      unless features_equal
-        feature_new.put 
-      end
-      feature
-    end
-
-    # Find out feature type
-    # Classification takes precedence
-    # @return [String] Feature type
-    def feature_type
-      bad_request_error "rdf type of feature '#{@uri}' not set" unless self[RDF.type]
-      if self[RDF.type].include?(OT.NominalFeature)
-        "classification"
-      elsif [RDF.type].to_a.flatten.include?(OT.NumericFeature)
-        "regression"
-      else
-        "unknown"
-      end
-    end
-
-    # Get accept values
-    # @param[String] Feature URI
-    # @return[Array] Accept values
-    def accept_values
-      accept_values = self[OT.acceptValue]
-      accept_values.sort if accept_values
-      accept_values
-    end
-
-  end
-
-end
diff --git a/lib/utils/shims/opentox.rb b/lib/utils/shims/opentox.rb
deleted file mode 100644
index c10d535..0000000
--- a/lib/utils/shims/opentox.rb
+++ /dev/null
@@ -1,51 +0,0 @@
-=begin
-* Name: opentox.rb
-* Description: Architecture shims
-* Author: Andreas Maunz <andreas@maunz.de>
-* Date: 10/2012
-=end
-
-# This avoids having to prefix everything with "RDF::" (e.g. "RDF::DC").
-# So that we can use our old code mostly as is.
-include RDF
-
-module OpenTox
-
-    # Help function to provide the metadata= functionality.
-    # Downward compatible to opentox-ruby.
-    # @param [Hash] Key-Value pairs with the metadata
-    # @return self
-    def metadata=(hsh) 
-      hsh.each {|k,v|
-        self[k]=v
-      }
-    end
-
-
-    ### Index Structures
-    
-    # Create parameter positions map
-    # @return [Hash] A hash with keys parameter names and values parameter positions
-    def build_parameter_positions
-      unless @parameter_positions
-        @parameters = parameters
-        @parameter_positions = @parameters.each_index.inject({}) { |h,idx|
-          h[@parameters[idx][DC.title.to_s]] = idx
-          h
-        }
-      end
-    end
-
-
-    ### Associative Search Operations
-    
-    # Search a model for a given parameter
-    # @param[String] The parameter title
-    # @return[Object] The parameter value
-    def find_parameter_value(title)
-      build_parameter_positions
-      res = @parameters[@parameter_positions[title]][OT.paramValue.to_s] if @parameter_positions[title]
-      res
-    end
-
-end
author	Andreas Maunz <andreas@maunz.de>	2012-10-24 16:35:31 +0200
committer	Andreas Maunz <andreas@maunz.de>	2012-10-24 16:35:31 +0200
commit	ad1725a4ee950b15d9d7c5d10a56babd0ae3706a (patch)
tree	f760ee460f2fd16022970013e4d75e9263977169
parent	9b86169dfb87e60c81ae4dd55312cdb5b1b9d2e9 (diff)