Merged shims

author: Andreas Maunz <andreas@maunz.de> 2012-10-24 16:35:09 +0200
committer: Andreas Maunz <andreas@maunz.de> 2012-10-24 16:35:09 +0200
commit: 9c8b20a910d316c19d24e79dcf52868b6b8383b7 (patch)
tree: d5f4bf89f7e77d452e1b48709449556afea5ffb4 /lib
parent: d182e4f3d666ad2586161c2ae84775148d3c11ad (diff)
7 files changed, 327 insertions, 0 deletions
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index d08d07a..67e0ce7 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -39,3 +39,6 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m
   "algorithm.rb"
 ].each{ |f| require File.join(File.dirname(__FILE__),f) }
 
+Dir["#{File.dirname(__FILE__)}/utils/shims/*.rb"].each { |f| require f } # Shims for legacy code
+Dir["#{File.dirname(__FILE__)}/utils/*.rb"].each { |f| require f } # Utils for Libs
+
diff --git a/lib/utils/diag.rb b/lib/utils/diag.rb
new file mode 100644
index 0000000..fd37945
--- /dev/null
+++ b/lib/utils/diag.rb
@@ -0,0 +1,11 @@
+=begin
+* Name: diag.rb
+* Description: Diagnostic tools
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
+# Print a diagnostic message
+def uri_list 
+  puts "My load path is:\n#{$LOAD_PATH.join("\n")} \nI have loaded #{$LOADED_FEATURES.size} objects.\n\n"
+end
diff --git a/lib/utils/html.rb b/lib/utils/html.rb
new file mode 100644
index 0000000..91dfc64
--- /dev/null
+++ b/lib/utils/html.rb
@@ -0,0 +1,49 @@
+#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
+
+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/dataset.rb b/lib/utils/shims/dataset.rb
new file mode 100644
index 0000000..75948e0
--- /dev/null
+++ b/lib/utils/shims/dataset.rb
@@ -0,0 +1,104 @@
+=begin
+* Name: dataset.rb
+* Description: Dataset shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
+module OpenTox
+
+  # Shims for the Dataset Class
+  class Dataset
+
+    attr_accessor :feature_positions, :compound_positions
+
+    # Load a dataset from URI
+    # @param [String] Dataset URI
+    # @return [OpenTox::Dataset] Dataset object
+    def self.find(uri, subjectid=nil)
+      return nil unless uri
+      ds = OpenTox::Dataset.new uri, subjectid
+      ds.get
+      ds
+    end
+
+
+
+    ### Index Structures
+
+    # Create value map
+    # @param [OpenTox::Feature] A feature
+    # @return [Hash] A hash with keys 1...feature.training_classes.size and values training classes
+    def value_map(feature)
+      training_classes = feature.accept_values
+      training_classes.each_index.inject({}) { |h,idx| h[idx+1]=training_classes[idx]; h } 
+    end
+
+    # Create feature positions map
+    # @return [Hash] A hash with keys feature uris and values feature positions
+    def build_feature_positions
+      unless @feature_positions
+        @feature_positions = @features.each_index.inject({}) { |h,idx| 
+          internal_server_error "Duplicate Feature '#{@features[idx].uri}' in dataset '#{@uri}'" if h[@features[idx].uri]
+          h[@features[idx].uri] = idx 
+          h
+        }
+      end
+    end
+
+    # Create compounds positions map
+    # @return [Hash] A hash with keys compound uris and values compound position arrays
+    def build_compound_positions
+      unless @compound_positions
+        @compound_positions = @compounds.each_index.inject({}) { |h,idx| 
+          inchi=OpenTox::Compound.new(@compounds[idx].uri).inchi
+          h[inchi] = [] unless h[inchi]
+          h[inchi] << idx if inchi =~ /InChI/
+          h
+        }
+      end
+    end
+
+
+    ### Associative Search Operations
+
+    # Search a dataset for a feature given its URI
+    # @param [String] Feature URI
+    # @return [OpenTox::Feature] Feature object, or nil if not present
+    def find_feature(uri)
+      build_feature_positions
+      res = @features[@feature_positions[uri]] if @feature_positions[uri]
+      res
+    end
+
+    # Search a dataset for a compound given its URI
+    # @param [String] Compound URI
+    # @return [OpenTox::Compound] Array of compound objects, or nil if not present
+    def find_compound(uri)
+      build_compound_positions
+      inchi = OpenTox::Compound.new(uri).inchi
+      res = @compounds[@compound_positions[inchi]] if inchi =~ /InChI/ and @compound_positions[inchi]
+      res
+    end
+
+    # Search a dataset for a data entry given compound URI and feature URI
+    # @param [String] Compound URI
+    # @param [String] Feature URI
+    # @return [Object] Data entry, or nil if not present
+    def find_data_entry(compound_uri, feature_uri)
+      build_compound_positions
+      build_feature_positions
+      inchi = OpenTox::Compound.new(compound_uri).inchi
+      if @compound_positions[inchi] && @feature_positions[feature_uri]
+        res = []
+        @compound_positions[inchi].each { |idx|
+          res << data_entries[idx][@feature_positions[feature_uri]]
+        }
+      end
+      res
+    end
+
+  end
+
+
+end
diff --git a/lib/utils/shims/feature.rb b/lib/utils/shims/feature.rb
new file mode 100644
index 0000000..297748b
--- /dev/null
+++ b/lib/utils/shims/feature.rb
@@ -0,0 +1,87 @@
+=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
new file mode 100644
index 0000000..c10d535
--- /dev/null
+++ b/lib/utils/shims/opentox.rb
@@ -0,0 +1,51 @@
+=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
diff --git a/lib/utils/shims/task.rb b/lib/utils/shims/task.rb
new file mode 100644
index 0000000..cb73e72
--- /dev/null
+++ b/lib/utils/shims/task.rb
@@ -0,0 +1,22 @@
+=begin
+* Name: task.rb
+* Description: Task shims
+* Author: Andreas Maunz <andreas@maunz.de>
+* Date: 10/2012
+=end
+
+
+module OpenTox
+
+  # Shims for the Task class
+  class Task
+
+    # Check status of a task
+    # @return [String] Status
+    def status
+      self[RDF::OT.hasStatus]
+    end
+
+  end
+
+end
author	Andreas Maunz <andreas@maunz.de>	2012-10-24 16:35:09 +0200
committer	Andreas Maunz <andreas@maunz.de>	2012-10-24 16:35:09 +0200
commit	9c8b20a910d316c19d24e79dcf52868b6b8383b7 (patch)
tree	d5f4bf89f7e77d452e1b48709449556afea5ffb4 /lib
parent	d182e4f3d666ad2586161c2ae84775148d3c11ad (diff)