Module: OpenTox

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

Defined Under Namespace

Modules: Algorithm, Authorization, Model, OntologyService, Parser, Serializer Classes: BadRequestError, Compound, Crossvalidation, CrossvalidationReport, Dataset, ErrorReport, FakeSubTask, Feature, LazarPrediction, NotAuthorizedError, NotFoundError, Policies, Policy, QMRFReport, 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.



4
5
6
 
# File 'lib/opentox.rb', line 4

def metadata
  @metadata
end

#uri ⇒ Object

Returns the value of attribute uri.



3
4
5
 
# 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



22
23
24
 
# 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

.login(msg = nil) ⇒ Object 



70
71
72
73
74
75
76
77
78
79
80
81
82
83
 
# File 'lib/to-html.rb', line 70

def self.( msg=nil )
  html = "<html><title>Login</title><img src="++"><body>"
  html += "<form method='POST' action='"+$url_provider.url_for("/login",:full)+"'>"
  html += "<pre><p style=\"padding:15px; border:10px solid \#5D308A\">"
  html += msg+"\n\n" if msg
  html += "Please login to "+$url_provider.url_for("",:full)+"\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='Login' /></td></tr>"
  html += "</table></p></pre></form></body><html>"
  html
end

.text_to_html(text, subjectid = nil, related_links = nil, description = nil, post_params = 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

[ [:mandatory_param_1], [:mandatory_param_2], [:optional_param,“default_value”

],

[:alteranative_mandatory_param_1], [:alteranative_mandatory_param_2

]

]

Examples:

post params:

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_params, (optional, Array) —

    array of arrays containing info on POST operation, see example

Returns:



27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
 
# File 'lib/to-html.rb', line 27

def self.text_to_html( text, subjectid=nil, related_links=nil, description=nil, post_params=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="++"><body>"
    
  if AA_SERVER
    user = OpenTox::Authorization.get_user(subjectid) if subjectid
    html +=  "<pre><p align=\"right\">"
    unless user
      html += "You are currently not logged in to "+$url_provider.url_for("",:full)+
        ", <a href="+$url_provider.url_for("/login",:full)+">login</a>"
    else
      html += "You are logged in as '#{user}' to "+$url_provider.url_for("",:full)+
        ", <a href="+$url_provider.url_for("/logout",:full)+">logout</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_params
    html += "<h3>POST parameters</h3>"
    count = 0
    post_params.each do |p|
      html += "<pre><p>alternatively:</p></pre>" if count > 0
      html += "<pre><p><table><thead><tr><th>param</th><th>default_value</th></tr></thead>"
      p.each do |k,v|
        html += "<tr><th>"+k.to_s+"</th><th>"+(v!=nil ? v.to_s : "<i>mandatory</i>")+"</th></tr>"
      end
      html += "</table></p></pre>"
      count += 1
    end
  end
  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

Instance Method Details

#add_metadata(metadata) ⇒ Object 



33
34
35
 
# File 'lib/opentox.rb', line 33

def add_metadata(metadata)
  metadata.each { |k,v| @metadata[k] = v }
end

#delete(subjectid = nil) ⇒ Object

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



47
48
49
 
# File 'lib/opentox.rb', line 47

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

#initialize(uri = nil) ⇒ Object

Initialize OpenTox object with optional uri

Parameters:



8
9
10
11
 
# 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



28
29
30
31
 
# 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



39
40
41
42
43
44
 
# File 'lib/opentox.rb', line 39

def to_rdfxml
  s = Serializer::Owl.new
  s.add_metadata(@uri,@metadata)
  #s.add_parameters(@uri,@parameters) if @parameters
  s.to_rdfxml
end