Module: OpenTox

Included in:
Algorithm, AlgorithmComparisonReport, Compound, Crossvalidation, CrossvalidationReport, Dataset, Feature, Model, QMRFReport, Task, Validation, ValidationReport
Defined in:
lib/task.rb,
lib/error.rb,
lib/model.rb,
lib/utils.rb,
lib/parser.rb,
lib/policy.rb,
lib/r-util.rb,
lib/dataset.rb,
lib/feature.rb,
lib/opentox.rb,
lib/to-html.rb,
lib/compound.rb,
lib/ontology.rb,
lib/algorithm.rb,
lib/transform.rb,
lib/serializer.rb,
lib/validation.rb,
lib/authorization.rb,
lib/rest_client_wrapper.rb

Defined Under Namespace

Modules: Algorithm, Authorization, Model, Ontology, Parser, Serializer, Transform Classes: AlgorithmComparisonReport, BadRequestError, Compound, Crossvalidation, CrossvalidationReport, Dataset, ErrorReport, FakeSubTask, Feature, LazarPrediction, NotAuthorizedError, NotFoundError, Policies, Policy, PostAttribute, PostCommand, QMRFReport, RUtil, RestCallError, RestClientWrapper, ServiceUnavailableError, SubTask, Task, Validation, ValidationReport, WrapperResult

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#metadata ⇒ Object

Returns the value of attribute metadata.



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# File 'lib/opentox.rb', line 4

def metadata
  @metadata
end

#uri ⇒ Object

Returns the value of attribute uri.



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# File 'lib/opentox.rb', line 3

def uri
  @uri
end

Class Method Details

.all(uri, subjectid = nil) ⇒ Array

Get all objects from a service

Returns:

  • (Array) —

    List of available URIs



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# File 'lib/opentox.rb', line 22

def self.all(uri, subjectid=nil)
  RestClientWrapper.get(uri,:accept => "text/uri-list", :subjectid => subjectid).to_s.split(/\n/)
end

.sign_in(msg = nil) ⇒ Object 



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# File 'lib/to-html.rb', line 59

def self.( msg=nil )
  html = "<html><title>Login</title><img src="+OT_LOGO+"><body>"
  html += "<form method='POST' action='"+$url_provider.url_for("/sign_in",:full)+"'>"
  html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
  html += msg+"\n\n" if msg
  html += "Please sign in to "+$url_provider.request.host.to_s+"\n\n"
  html += "<table border=0>"
  html += "<tr><td>user:</td><td><input type='text' name='user' size='15' /></td></tr>"+
        "<tr><td>password:</td><td><input type='password' name='password' size='15' /></td></tr>"+
        #"<input type=hidden name=back_to value="+back_to.to_s+">"+
        "<tr><td><input type='submit' value='Sign in' /></td></tr>"
  html += "</table></p></pre></form></body></html>"
  html
end

.text_to_html(text, subjectid = nil, related_links = nil, description = nil, post_command = nil) ⇒ String

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

Parameters:

  • text (String) —

    this is the actual content,

  • related_links (optional, String) (defaults to: nil) —

    info on related resources

  • description (optional, String) (defaults to: nil) —

    general info

  • post_command, (optional, Array) —

    infos for the post operation, object defined below

Returns:



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# File 'lib/to-html.rb', line 24

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>"
    
  if AA_SERVER
    user = OpenTox::Authorization.get_user(subjectid) if subjectid
    html +=  "<pre><p align=\"right\">"
    unless user
      html += "You are currently not signed in to "+$url_provider.request.host.to_s+
        ", <a href="+$url_provider.url_for("/sign_in",:full)+">sign in</a>"
    else
      html += "You are signed in as '#{user}' to "+$url_provider.request.host.to_s+
        ", <a href="+$url_provider.url_for("/sign_out",:full)+">sign out</a>"
    end
    html += "  </p></pre>"
  end 
 
  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
  if post_command
    raise "not a post command" unless post_command.is_a?(OpenTox::PostCommand)
    html += "<h3>POST command</h3>"
    html += post_command.to_html
  end
  html += "<h3>Content</h3>" if description || related_links || post_command
  html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
  html += text.link_urls
  html += "</p></pre></body></html>"
  html
end

Instance Method Details

#add_metadata(metadata) ⇒ Object 



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# File 'lib/opentox.rb', line 33

def add_metadata(metadata)
  if !metadata.nil?
    metadata.each do |k,v|
      if v.is_a? Array
        @metadata[k] = [] unless @metadata[k]
        @metadata[k] << v
      else
        @metadata[k] = v 
      end
    end
  end
end

#delete(subjectid = nil) ⇒ Object

deletes the resource, deletion should have worked when no RestCallError raised



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# File 'lib/opentox.rb', line 55

def delete(subjectid=nil)
  RestClientWrapper.delete(uri,:subjectid => subjectid)
end

#initialize(uri = nil) ⇒ Object

Initialize OpenTox object with optional uri

Parameters:



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# File 'lib/opentox.rb', line 8

def initialize(uri=nil)
  @metadata = {}
  self.uri = uri if uri
end

#load_metadata(subjectid = nil) ⇒ Hash

Load (and return) metadata from object URI

Returns:

  • (Hash) —

    Metadata



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# File 'lib/opentox.rb', line 28

def load_metadata(subjectid=nil)
  @metadata = Parser::Owl::Generic.new(@uri).load_metadata(subjectid)
  @metadata
end

#to_rdfxml ⇒ application/rdf+xml

Get OWL-DL representation in RDF/XML format

Returns:

  • (application/rdf+xml) —

    RDF/XML representation



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# File 'lib/feature.rb', line 48

def to_rdfxml
  s = Serializer::Owl.new
  s.add_feature(@uri,@metadata)
  @metadata.values.grep(/model\/\d+$/).each{ |m| s.add_uri(m,OT.Model)}
  @metadata.values.grep(/feature/).each{ |f| s.add_uri(f,OT.Feature)}
  #s.add_parameters(@uri,@parameters) if @parameters
  s.to_rdfxml
end