opentox-ruby 3.0.0 → 3.0.1

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Files changed (5) hide show
  1. data/ChangeLog +5 -0
  2. data/VERSION +1 -1
  3. data/lib/authorization.rb +1 -1
  4. data/lib/ontology.rb +16 -27
  5. metadata +6 -4
@@ -0,0 +1,5 @@
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+ v3.0.1 2011-10-19
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+ * feature: model registration to ontology service
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+ * ontology lib gets endpoints from ontology service
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+ v3.0.0 2011-09-23
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+ * datasets stored as json (with Yajl) to improve performance
data/VERSION CHANGED
@@ -1 +1 @@
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- 3.0.0
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+ 3.0.1
@@ -319,7 +319,7 @@ module OpenTox
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  # if policy exists check for POST rights
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  if authorize(uri, "POST", subjectid)
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  true
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- else
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+ else
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  LOGGER.error "OpenTox::Authorization.check_policy, already exists, but no POST-authorization with subjectid: #{subjectid}"
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  false
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  end
@@ -4,13 +4,9 @@ module OpenTox
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  def self.querystring(classname="Endpoints")
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  return CGI.escape("PREFIX ot:<http://www.opentox.org/api/1.1#>
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- PREFIX ota:<http://www.opentox.org/algorithms.owl#>
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- PREFIX owl:<http://www.w3.org/2002/07/owl#>
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  PREFIX dc:<http://purl.org/dc/elements/1.1/>
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  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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- PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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  PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
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- PREFIX toxcast:<http://www.opentox.org/toxcast.owl#>
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  select *
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  where {
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  ?endpoint rdfs:subClassOf otee:#{classname}.
@@ -18,25 +14,22 @@ module OpenTox
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  }")
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  end
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- def self.make_option_list(endpoint="Endpoints", level=1)
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- out = ""
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- results = echa_endpoints(endpoint) rescue results = []
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- results.each do |result|
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- r = result.split(',')
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- endpointname = r.first.split("#").last
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- title = r[1..r.size-1]
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- out += "<option value='#{r.first}' id='#{endpointname}' class='level_#{level}'>#{title}</option>\n"
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- out += make_option_list(endpointname, level + 1)
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+ # Gets Endpoint name of a specific endpoint URI
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+ # @param [String] endpointuri e.G. "http://www.opentox.org/echaEndpoints.owl#EcotoxicEffects"
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+ # @return [String] endpointname: e.G.: "Ecotoxic effects"
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+ def self.get_endpoint_name(endpointuri)
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+ qstring = CGI.escape("PREFIX dc:<http://purl.org/dc/elements/1.1/>
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+ select distinct ?title
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+ where {
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+ ?endpoint dc:title ?title.
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+ FILTER (?endpoint = <#{endpointuri}>)
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+ }")
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+ begin
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+ RestClientWrapper.get("#{ONTOLOGY_SERVER}?query=#{qstring}",:accept => "text/csv").collect{|l| l.gsub("\r\n", "") if l.to_s != "title\r\n"}.uniq.compact.sort.first.to_s
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+ rescue
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+ LOGGER.warn "OpenTox::Ontology::Echa.get_endpoint_name(#{endpointuri}) ontology service is not reachable."
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+ []
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  end
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- return out
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- end
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-
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- def self.endpoint_option_list(include_blank=true)
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- out = "<select id='endpoint' name='endpoint'>\n"
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- out += "<option value='' id='please_select'>Please select</option>\n" if include_blank
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- out += make_option_list
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- out += "</select>\n"
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- return out
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  end
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  # Gets Endpoints of specific level from ontology service
@@ -115,11 +108,8 @@ module OpenTox
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  # Query string to find a registered model
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  # @param [String] uri, model URI
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  def self.querystring(uri)
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- return CGI.escape("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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- PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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- PREFIX owl:<http://www.w3.org/2002/07/owl#>
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+ return CGI.escape("PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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  PREFIX dc:<http://purl.org/dc/elements/1.1/>
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- PREFIX dcterms:<http://purl.org/dc/terms/>
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  PREFIX ot:<http://www.opentox.org/api/1.1#>
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  select distinct ?model ?title ?creator ?trainingDataset ?algorithm
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  where {
@@ -132,6 +122,5 @@ module OpenTox
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  }")
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  end
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  end
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-
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  end
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  end
metadata CHANGED
@@ -1,13 +1,13 @@
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  --- !ruby/object:Gem::Specification
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  name: opentox-ruby
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  version: !ruby/object:Gem::Version
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- hash: 7
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+ hash: 5
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  prerelease:
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  segments:
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  - 3
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  - 0
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- - 0
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- version: 3.0.0
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+ - 1
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+ version: 3.0.1
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  platform: ruby
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  authors:
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  - Christoph Helma, Martin Guetlein, Andreas Maunz, Micha Rautenberg, David Vorgrimmler
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-09-26 00:00:00 +02:00
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+ date: 2011-10-24 00:00:00 +02:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -536,9 +536,11 @@ executables: []
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  extensions: []
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  extra_rdoc_files:
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+ - ChangeLog
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  - LICENSE
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  - README.markdown
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  files:
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+ - ChangeLog
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  - LICENSE
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  - README.markdown
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  - Rakefile